Re: [gmx-users] pdb2gmx

[Nikhil Maroli]

You need to check the archive or Google :
Residue 1 named LYS of a molecule in the input file was mapped

to an entry in the topology database, but the atom N used in
that entry is not found in the input file


You might need to change the naming of your atoms according the
forcefield your using
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello users,
I am using pdb2gmx on a protein.
Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
  N
0.00   H
ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
  N

These are N atoms in my LYS . Can anyone point out what the problem.



Please provide your exact pdb2gmx command and the full screen output.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[amitbehra]

Hi Justin,
Here is the full screen output:

Read 2236 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 285 residues with 2236 atoms

  chain  #res #atoms
  1 ' '   285   2236

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 (2236 atoms, 285 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 412 donors and 445 acceptors were found.
There are 574 hydrogen bonds
Will use HISE for residue 292
Identified residue LYS8 as a starting terminus.
Identified residue HIS292 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   MET70   CYS87  MET270  MET281  CYS285
   SD500   SG649  SD2051  SD2135  SG2165
   CYS87   SG649   2.813
  MET270  SD2051   5.200   2.414
  MET281  SD2135   3.579   0.855   1.703
  CYS285  SG2165   3.012   0.370   2.301   0.930
  HIS292 NE22232   1.990   1.007   3.388   1.772   1.152
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127

Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

>>
>> Message: 7
>> Date: Fri, 19 Aug 2016 15:30:14 -0400
>> From: Justin Lemkul 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] pdb2gmx
>> Message-ID: 
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:
>>> Hello users,
>>> I am using pdb2gmx on a protein.
>>> Fatal error:
>>> Residue 1 named LYS of a molecule in the input file was mapped
>>> to an entry in the topology database, but the atom N used in
>>> that entry is not found in the input file. Perhaps your atom
>>> and/or residue naming needs to be fixed.
>>>
>>> ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
>>>   N
>>> 0.00   H
>>> ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
>>>   N
>>>
>>> These are N atoms in my LYS . Can anyone point out what the problem.
>>>
>>
>> Please provide your exact pdb2gmx command and the full screen output.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)sub

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 8/20/16 1:57 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hi Justin,
Here is the full screen output:

Read 2236 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 285 residues with 2236 atoms

  chain  #res #atoms
  1 ' '   285   2236

All occupancies are one
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 (2236 atoms, 285 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 412 donors and 445 acceptors were found.
There are 574 hydrogen bonds
Will use HISE for residue 292
Identified residue LYS8 as a starting terminus.
Identified residue HIS292 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
   MET70   CYS87  MET270  MET281  CYS285
   SD500   SG649  SD2051  SD2135  SG2165
   CYS87   SG649   2.813
  MET270  SD2051   5.200   2.414
  MET281  SD2135   3.579   0.855   1.703
  CYS285  SG2165   3.012   0.370   2.301   0.930
  HIS292 NE22232   1.990   1.007   3.388   1.772   1.152
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file
/usr/local/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file:
/home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c,
line: 127

Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.



First it was N, now it's CA?  What happened to the error about N?  Only the 
first missing atom should trigger a fatal error.  There's nothing obvious to me 
from the provided information about why it's failing, so check to make sure CA 
isn't missing, make sure that the PDB file is correctly formatted, and also 
consider your residue names.  AMBER uses N- and C-prefixed residues for termini 
(e.g. NLYS instead of LYS, CHIS instead of HIS) so you may have to manually 
rename the residues unless pdb2gmx does some magic under the hood (it may, I 
haven't checked in a while since I don't use the AMBER force fields).


-Justin



Message: 7
Date: Fri, 19 Aug 2016 15:30:14 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb2gmx
Message-ID: 
Content-Type: text/plain; charset=windows-1252; format=flowed



On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello users,
I am using pdb2gmx on a protein.
Fatal error:
Residue 1 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

ATOM  1  N   LYS 8  59.565  44.696  51.226  1.00  0.00
  N
0.00   H
ATOM 19  NZ  LYS 8  62.201  50.111  51.767  1.00  0.00
  N

These are N atoms in my LYS . Can anyone point out what the problem.



Please provide your exact pdb2gmx command and the full screen output.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==




--

--
Gromacs Users mailing list

* Please search the a

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 6/18/14, 11:18 AM, mirko busato wrote:

Dear Users,

I am using the command pdb2gmx_d on a neutral peptide in this way:

pdb2gmx_d -f pep2_n.pdb -water none -inter

My force field is AMBER. The first residue is ASN and the last residue is ARG
My terminals are not ionized (NH2 and COOH). So I changed the name of residue 
ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS 
in ACE for the  4 atoms (C,O2,O1,H2).

If in the interactive way I select ARG (not protonated) ,I obtained a message like 
that " Fatal error:
In the chosen force field there is no residue type for 'ARGN' ".

After I tried to select ARG(protonated) and I obtained this error: There is a 
dangling bond at at least one of the terminal ends and the force field does not 
provide terminal entries or files. Fix your terminal residues sothat they 
match the residue database (.rtp) entries, or provide terminal database entries 
(.tdb).

Could you help me?



If you have non-amino acids as the termini (i.e. capping groups), you need to 
select "None" for both termini.  The side chain protonation is irrelevant to the 
treatment of the actual termini.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[mirko busato]

Thank you very much for your quick reply,

My peptide is only composed of amino acids, and it has a total charge of 0.
My termini are NH2 and COOH (so the termini are not  ionized). My force field 
is amber99sb.
 
I tried to change  for all atoms of my first residue (ASN) the ASN residue with 
 the  NASN residue name. In the first residue (ASN) there are the 3 atoms of N 
terminal . In the same way for ARG (the last residue ) with CARG.

With -inter option  in the pdb2gmx command,
If I select Not protonated ARG (charge 0) and the other residues with charge 0, 
at the end the command says:
Fatal error
"In the chosen force field there is no residue type for 'ARGN' as an ending 
terminus"

if I select protonated ARG (charge 1) and the other residues  with charge 0, I 
obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and my 
COOH in COO. (The command works but in my case the result is wrong because the 
total charge has to be 0 with NH2 and COOH termini, not ionized).

I don't understand if in my case I have to change ASN to NASN only for the 3 
atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C 
terminal ( C,O2,O1,H)

or change for all atoms of the first residue (ASN), ASN with NASN, and change 
all atoms of the last residue (ARG) , ARG with CARG.( that I done and described 
before)..
 If this is the right way, I don't know how to obtain the right result for my 
peptide.

Could you help me?

I attached  my original .pdb file (not edited), and my edited pdb file.


Thank you very much, 

Mirko


On Wednesday, June 18, 2014 5:20 PM, Justin Lemkul  wrote:
 





On 6/18/14, 11:18 AM, mirko busato wrote:
> Dear Users,
>
> I am using the command pdb2gmx_d on a neutral peptide in this way:
>
> pdb2gmx_d -f pep2_n.pdb -water none -inter
>
> My force field is AMBER. The first residue is ASN and the last residue is ARG
> My terminals are not ionized (NH2 and COOH). So I changed the name of residue 
> ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS 
> in ACE for the  4 atoms (C,O2,O1,H2).
>
> If in the interactive way I select ARG (not protonated) ,I obtained a message 
> like that " Fatal error:
> In the chosen force field there is no residue type for 'ARGN' ".
>
> After I tried to select ARG(protonated) and I obtained this error: There is a 
> dangling bond at at least one of the terminal ends and the force field does 
> not provide terminal entries or files. Fix your terminal residues so    that 
> they match the residue database (.rtp) entries, or provide terminal database 
> entries (.tdb).
>
> Could you help me?
>

If you have non-amino acids as the termini (i.e. capping groups), you need to 
select "None" for both termini.  The side chain protonation is irrelevant to 
the 
treatment of the actual termini.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 6/19/14, 8:59 AM, mirko busato wrote:

Thank you very much for your quick reply,

My peptide is only composed of amino acids, and it has a total charge of 0.
My termini are NH2 and COOH (so the termini are not  ionized). My force field is
amber99sb.
I tried to change  for all atoms of my first residue (ASN) the ASN residue with
  the  NASN residue name. In the first residue (ASN) there are the 3 atoms of N
terminal . In the same way for ARG (the last residue ) with CARG.



Look at the force field .rtp file - you will see that the Amber termini are 
predefined and they are always charged.  That is an unfortunate limitation to 
the current implementation.  I suspect someone must have produced neutral forms 
of the termini, but you'll have to add them yourself if you want to do such a 
simulation with this force field.



With -inter option  in the pdb2gmx command,
If I select Not protonated ARG (charge 0) and the other residues with charge 0,
at the end the command says:
Fatal error
"In the chosen force field there is no residue type for 'ARGN' as an ending
terminus"



This option chooses the side chain protonation state, not the terminus.


if I select protonated ARG (charge 1) and the other residues  with charge 0, I
obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and my
COOH in COO. (The command works but in my case the result is wrong because the
total charge has to be 0 with NH2 and COOH termini, not ionized).

I don't understand if in my case I have to change ASN to NASN only for the 3
atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C
terminal ( C,O2,O1,H)

or change for all atoms of the first residue (ASN), ASN with NASN, and change
all atoms of the last residue (ARG) , ARG with CARG.( that I done and described
before)..
  If this is the right way, I don't know how to obtain the right result for my
peptide.



As stated above, you'll have to modify the force field to add appropriate 
parameters or otherwise use a different force field that actually allows you to 
choose terminus protonation state.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[mirko busato]

Thank you,

I understood,  you are right, in the .rtp file  there are not neutral form for 
the termini.

What can I do to have a neutral arginine, to have at least a total charge of 0?

Because In my case I am forced to choose ARG protonated else I get the error.

Fatal error
"In the chosen force field there is no residue type for 'ARGN' as an ending
 terminus"

Thank you very much,

Mirko
On Thursday, June 19, 2014 3:17 PM, Justin Lemkul  wrote:
 




On 6/19/14, 8:59 AM, mirko busato wrote:
> Thank you very much for your quick reply,
>
> My peptide is only composed of amino acids, and it has a total charge of 0.
> My termini are NH2 and COOH (so the termini are not  ionized). My force field 
> is
> amber99sb.
> I tried to change  for all atoms of my first residue (ASN) the ASN residue 
> with
>   the  NASN residue name. In the first residue (ASN) there are the 3 atoms of 
>N
> terminal . In the same way for ARG (the last residue ) with CARG.
>

Look at the force field .rtp file - you will see that the Amber termini are 
predefined and they are always charged.  That is an unfortunate limitation to 
the current implementation.  I suspect someone must have produced neutral forms 
of the termini, but you'll have to add them yourself if you want to do such a 
simulation with this force field.

> With -inter option  in the pdb2gmx command,
> If I select Not protonated ARG (charge 0) and the other residues with charge 
> 0,
> at the end the command says:
> Fatal error
> "In the chosen force field there is no
 residue type for 'ARGN' as an ending
> terminus"
>

This option chooses the side chain protonation state, not the terminus.

> if I select protonated ARG (charge 1) and the other residues  with charge 0, I
> obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and my
> COOH in COO. (The command works but in my case the result is wrong because the
> total charge has to be 0 with NH2 and COOH termini, not ionized).
>
> I don't understand if in my case I have to change ASN to NASN only for the 3
>
 atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms in C
> terminal ( C,O2,O1,H)
>
> or change for all atoms of the first residue (ASN), ASN with NASN, and change
> all atoms of the last residue (ARG) , ARG with CARG.( that I done and 
> described
> before)..
>   If this is the right way, I don't know how to obtain the right result for my
> peptide.
>

As stated above, you'll have to modify the force field to add appropriate 
parameters or otherwise use a different force field that actually allows you to 
choose terminus protonation state.


-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 6/20/14, 10:12 AM, mirko busato wrote:

Thank you,

I understood,  you are right, in the .rtp file  there are not neutral form for
the termini.

What can I do to have a neutral arginine, to have at least a total charge of 0?

Because In my case I am forced to choose ARG protonated else I get the error.

Fatal error
"In the chosen force field there is no residue type for 'ARGN' as an ending
  terminus"



Use a force field that has parameters for a neutral form.  I'm sure someone has 
produced parameters for such a species, but they're not included in Amber99SB by 
default.  If parameters are out there, add them 
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), otherwise 
use a different force field.


-Justin


Thank you very much,

Mirko
On Thursday, June 19, 2014 3:17 PM, Justin Lemkul  wrote:




On 6/19/14, 8:59 AM, mirko busato wrote:
 > Thank you very much for your quick reply,
 >
 > My peptide is only composed of amino acids, and it has a total charge of 0.
 > My termini are NH2 and COOH (so the termini are not  ionized). My force 
field is
 > amber99sb.
 > I tried to change  for all atoms of my first residue (ASN) the ASN residue 
with
 >  the  NASN residue name. In the first residue (ASN) there are the 3 atoms of 
N
 > terminal . In the same way for ARG (the last residue ) with CARG.
 >

Look at the force field .rtp file - you will see that the Amber termini are
predefined and they are always charged.  That is an unfortunate limitation to
the current implementation.  I suspect someone must have produced neutral forms
of the termini, but you'll have to add them yourself if you want to do such a
simulation with this force field.

 > With -inter option  in the pdb2gmx command,
 > If I select Not protonated ARG (charge 0) and the other residues with charge 
0,
 > at the end the command says:
 > Fatal error
 > "In the chosen force field there is no residue type for 'ARGN' as an ending
 > terminus"
 >

This option chooses the side chain protonation state, not the terminus.

 > if I select protonated ARG (charge 1) and the other residues  with charge 0, 
I
 > obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and my
 > COOH in COO. (The command works but in my case the result is wrong because 
the
 > total charge has to be 0 with NH2 and COOH termini, not ionized).
 >
 > I don't understand if in my case I have to change ASN to NASN only for the 3
 > atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms 
in C
 > terminal ( C,O2,O1,H)
 >
 > or change for all atoms of the first residue (ASN), ASN with NASN, and change
 > all atoms of the last residue (ARG) , ARG with CARG.( that I done and 
described
 > before)..
 >  If this is the right way, I don't know how to obtain the right result for my
 > peptide.
 >

As stated above, you'll have to modify the force field to add appropriate
parameters or otherwise use a different force field that actually allows you to
choose terminus protonation state.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[mirko busato]

Thank you very much,

In my analysis ,I would like to consider Hydrogen bonds involving S atom as 
well.  I think that g_hbond is not built to manage Hydrogen bonds with S.

Do you know if there are available scripts? or Could you suggest me something 
to solve this problem?

I really appreciate your help

Mirko



On Friday, June 20, 2014 4:17 PM, Justin Lemkul  wrote:
 




On 6/20/14, 10:12 AM, mirko busato wrote:
> Thank you,
>
> I understood,  you are right, in the .rtp file  there are not neutral form for
> the termini.
>
> What can I do to have a neutral arginine, to have at least a total charge of 
> 0?
>
> Because In my case I am forced to choose ARG protonated else I get the error.
>
> Fatal error
> "In the chosen force field there is no residue type for 'ARGN' as an ending
>   terminus"
>

Use a force field that has parameters for a neutral form.  I'm sure someone has 
produced parameters for such a species, but they're not included in Amber99SB 
by 
default.  If parameters are out there, add them 
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field),
 otherwise 
use a different force field.

-Justin

> Thank you very much,
>
> Mirko
> On Thursday, June 19, 2014 3:17 PM, Justin Lemkul  wrote:
>
>
>
>
> On 6/19/14, 8:59 AM, mirko busato wrote:
>  > Thank you very much for your quick reply,
>  >
>  > My peptide is only composed of amino acids, and it has a total charge of 0.
>  > My termini are NH2 and COOH (so the termini are not  ionized). My force 
>field is
>  > amber99sb.
>  > I tried to change  for all atoms of my first residue (ASN) the ASN residue 
>with
>  >  the  NASN residue name. In the first residue (ASN) there are the 3 atoms 
>of N
>  > terminal . In the same way for ARG (the last residue ) with CARG.
>  >
>
> Look at the force field .rtp file - you will see that the Amber termini are
> predefined and they are always charged.  That is an unfortunate limitation to
> the current implementation.  I suspect someone must have produced neutral 
> forms
> of the termini, but you'll have to add them yourself if you want to do such a
> simulation with this force field.
>
>  > With -inter option  in the pdb2gmx command,
>  > If I select Not protonated ARG (charge 0) and the other residues with 
>charge 0,
>  > at the end the command says:
>  > Fatal error
>  > "In the chosen force field there is no residue type for 'ARGN' as an ending
>  > terminus"
>  >
>
> This option chooses the side chain protonation state, not the terminus.
>
>  > if I select protonated ARG (charge 1) and the other residues  with charge 
>0, I
>  > obtain charge 1 (it is obvious) but my NH2  termini  is changed to NH3 and 
>my
>  > COOH in COO. (The command works but in my case the result is wrong because 
>the
>  > total charge has to be 0 with NH2 and COOH termini, not ionized).
>  >
>  > I don't understand if in my case I have to change ASN to NASN only for the 
>3
>  > atoms in N terminal( N,H,H) and to change ARG to CARG only for the 4 atoms 
>in C
>  > terminal ( C,O2,O1,H)
>  >
>  > or change for all atoms of the first residue (ASN), ASN with NASN, and 
>change
>  > all atoms of the last residue (ARG) , ARG with CARG.( that I done and 
>described
>  > before)..
>  >  If this is the right way, I don't know how to obtain the right result for 
>my
>  > peptide.
>  >
>
> As stated above, you'll have to modify the force field to add appropriate
> parameters or otherwise use a different force field that actually allows you 
> to
> choose terminus protonation state.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu  |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul

>
> ==
>
>

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before postin

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 6/25/14, 4:44 AM, mirko busato wrote:

Thank you very much,

In my analysis ,I would like to consider Hydrogen bonds involving S atom as 
well.  I think that g_hbond is not built to manage Hydrogen bonds with S.

Do you know if there are available scripts? or Could you suggest me something 
to solve this problem?



g_hbond is hard-coded to deal with certain groups, so it's not very flexible. 
The workaround we've used in the past is to simply rename the S atoms of 
interest as O in the .top file, generate a .tpr with those dummy names, and run 
g_hbond using that .tpr file.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[mirko busato]

Thank you very much,

I have one question for you. I would  like to  extract some information about 
salt bridge interactions (without using the gromacs command g_saltbr  because 
it gave me some problems) between some atoms (charged negatively) of a type of 
monomer and some atoms (charged positively )of another type of monomer.

So I created the two lists of atoms with g_select,
and I made a file index like that:

[ N_CRL ]
 300  321  342  363  384  405  426  447  468  489  510  531  552  573  594 
 615  636  657  678  699  720  741  762  783  804  825  846  867  888  909 
 930  951  972  993 1014 1035 1056 1077 1098 1119 
[ OX_ITA ]
 168  181  194  207  220  233  246  259  272  285 
 
and then I used g_hbond to extract the contacts of these 2 lists of atoms 
within 4 Å.

in this way:

g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 
0.4


I noticed a strange thing, if I change the order of the groups in the index.ndx 
file,like that:

[ OX_ITA ]
 168  181  194  207  220  233  246  259  272  285
[ N_CRL ]
 300  321  342  363  384  405  426  447  468  489  510  531  552  573  594 
 615  636  657  678  699  720  741  762  783  804  825  846  867  888  909 
 930  951  972  993 1014 1035 1056 1077 1098 1119 

I obtain no contacts, and it is wrong because actually I didn't change the 
atoms of the groups.

Could you help me about it ?

Thank you very much

Mirko


On Wednesday, June 25, 2014 12:00 PM, Justin Lemkul  wrote:
 




On 6/25/14, 4:44 AM, mirko busato wrote:
> Thank you very much,
>
> In my analysis ,I would like to consider Hydrogen bonds involving S atom as 
> well.  I think that g_hbond is not built to manage Hydrogen bonds with S.
>
> Do you know if there are available scripts? or Could you suggest me something 
> to solve this problem?
>

g_hbond is hard-coded to deal with certain groups, so it's not very flexible. 
The workaround we've used in the past is to simply rename the S atoms of 
interest as O in the .top file, generate a .tpr with those dummy names, and run 
g_hbond using that .tpr file.


-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Mark Abraham]

Hi,

The .rtp files are used by pdb2gmx in order to recognize residues in the
face of what can be massive noise in the input file. It primarily matches
names of atoms and residues. It writes a coordinate and topology file whose
atom and residue ordering matches each other, and whose atom types will
permit parameter lookup from the force field data bases - atom and residues
names become fairly (completely? idk) unimportant at this stage. I imagine
it is possible to duplicate the same atom name within a residue for use
with grompp, but likely there's no tool that generates such input for
grompp, because they need unique atom names so they can bring order from
chaos. Please check out the instructions and examples in Chapter 5 of the
manual.

Mark


On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll  wrote:

> Hello Gromacs users,
>
> I would like to add a molecule as a "residue" in the aminoacids.rtp file
> and I have a few questions.
>
> As far as I understand, a residue in a gro file can multiple atoms with the
> same "atom name." What links every atom in this residue to parameters in
> the top [ atoms ] directive is the *order.* The gro file "atom names" must
> match the top file atoms names but the mapping of parameters is done via
> the order, correct? This allows atoms in a residue to have the same "atom
> name" but be associated
> with a different "atom type," "charge group," etc...
>
> Does an entry in a residue database (e.g., aminoacids.rtp) work the same
> way?
> The syntax is shown below.
>
> [ TEST ]
> [ atoms ]
> ; atom_nameatom_typeatom_chargecharge_group
>
> I have to specify the "atom name," force field "atom type," "atom charge,"
> and "charge group" for every atom in the "TEST" residue in order. The "atom
> name" must match the "atom name" in the input coordinate file but the
> mapping is applied by the entry order, correct? I do no need unique "atom
> names," correct?
>
> Best,
> Eric
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Eric Smoll]

Hi Mark,

Thanks for your help. I am looking for a deeper understanding "residue
names," "atom names," and how they are used to properly form input for
grompp.

By experimentation, it appears the pdb2gmx requires unique "atom names"
within each residue of the .rtp file to properly process .gro/.pdb files.
Thus, every "atom name" of a residue in the .gro/.pdb file must be unique.
It this not made clear in the .rtp section of the manual. It also appears
that the bond directive is required, not optional as shown in the example
in the .rtp section of the manual.

However, if I build a system using an .itp file and the [ molecules ]
directive, the requirements are more flexible. Again, I observe that while
the "atoms names" of the gro and .itp files must match within a given
residue, they need not be unique. This is not made clear in the manual. It
seems (I hope) that matching is accomplished by the "nr" field of the
.top/,itp file and the "atom number" field of the .gro/.pdb file.

Best,
Eric

On Wed, Oct 29, 2014 at 3:56 AM, Mark Abraham 
wrote:

> Hi,
>
> The .rtp files are used by pdb2gmx in order to recognize residues in the
> face of what can be massive noise in the input file. It primarily matches
> names of atoms and residues. It writes a coordinate and topology file whose
> atom and residue ordering matches each other, and whose atom types will
> permit parameter lookup from the force field data bases - atom and residues
> names become fairly (completely? idk) unimportant at this stage. I imagine
> it is possible to duplicate the same atom name within a residue for use
> with grompp, but likely there's no tool that generates such input for
> grompp, because they need unique atom names so they can bring order from
> chaos. Please check out the instructions and examples in Chapter 5 of the
> manual.
>
> Mark
>
>
> On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll  wrote:
>
> > Hello Gromacs users,
> >
> > I would like to add a molecule as a "residue" in the aminoacids.rtp file
> > and I have a few questions.
> >
> > As far as I understand, a residue in a gro file can multiple atoms with
> the
> > same "atom name." What links every atom in this residue to parameters in
> > the top [ atoms ] directive is the *order.* The gro file "atom names"
> must
> > match the top file atoms names but the mapping of parameters is done via
> > the order, correct? This allows atoms in a residue to have the same "atom
> > name" but be associated
> > with a different "atom type," "charge group," etc...
> >
> > Does an entry in a residue database (e.g., aminoacids.rtp) work the same
> > way?
> > The syntax is shown below.
> >
> > [ TEST ]
> > [ atoms ]
> > ; atom_nameatom_typeatom_chargecharge_group
> >
> > I have to specify the "atom name," force field "atom type," "atom
> charge,"
> > and "charge group" for every atom in the "TEST" residue in order. The
> "atom
> > name" must match the "atom name" in the input coordinate file but the
> > mapping is applied by the entry order, correct? I do no need unique "atom
> > names," correct?
> >
> > Best,
> > Eric
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Eric Smoll]

Mark,

The discrepancy I describe is not a problem. As you mentioned, pdb2gmx is a
tool intended to process input files with a great deal of noise. This tool
can have its own requirements.

What is troublesome is that these differences lead me to question if
separate simulations with different input methods are making use of the
same parameters and that these parameters are correct.

If you are aware of any sanity checks the user can preform, that would be
most useful.

Best,
Eric

On Wed, Oct 29, 2014 at 10:55 AM, Eric Smoll  wrote:

> Hi Mark,
>
> Thanks for your help. I am looking for a deeper understanding "residue
> names," "atom names," and how they are used to properly form input for
> grompp.
>
> By experimentation, it appears the pdb2gmx requires unique "atom names"
> within each residue of the .rtp file to properly process .gro/.pdb files.
> Thus, every "atom name" of a residue in the .gro/.pdb file must be unique.
> It this not made clear in the .rtp section of the manual. It also appears
> that the bond directive is required, not optional as shown in the example
> in the .rtp section of the manual.
>
> However, if I build a system using an .itp file and the [ molecules ]
> directive, the requirements are more flexible. Again, I observe that while
> the "atoms names" of the gro and .itp files must match within a given
> residue, they need not be unique. This is not made clear in the manual. It
> seems (I hope) that matching is accomplished by the "nr" field of the
> .top/,itp file and the "atom number" field of the .gro/.pdb file.
>
> Best,
> Eric
>
> On Wed, Oct 29, 2014 at 3:56 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> The .rtp files are used by pdb2gmx in order to recognize residues in the
>> face of what can be massive noise in the input file. It primarily matches
>> names of atoms and residues. It writes a coordinate and topology file
>> whose
>> atom and residue ordering matches each other, and whose atom types will
>> permit parameter lookup from the force field data bases - atom and
>> residues
>> names become fairly (completely? idk) unimportant at this stage. I imagine
>> it is possible to duplicate the same atom name within a residue for use
>> with grompp, but likely there's no tool that generates such input for
>> grompp, because they need unique atom names so they can bring order from
>> chaos. Please check out the instructions and examples in Chapter 5 of the
>> manual.
>>
>> Mark
>>
>>
>> On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll  wrote:
>>
>> > Hello Gromacs users,
>> >
>> > I would like to add a molecule as a "residue" in the aminoacids.rtp file
>> > and I have a few questions.
>> >
>> > As far as I understand, a residue in a gro file can multiple atoms with
>> the
>> > same "atom name." What links every atom in this residue to parameters in
>> > the top [ atoms ] directive is the *order.* The gro file "atom names"
>> must
>> > match the top file atoms names but the mapping of parameters is done via
>> > the order, correct? This allows atoms in a residue to have the same
>> "atom
>> > name" but be associated
>> > with a different "atom type," "charge group," etc...
>> >
>> > Does an entry in a residue database (e.g., aminoacids.rtp) work the same
>> > way?
>> > The syntax is shown below.
>> >
>> > [ TEST ]
>> > [ atoms ]
>> > ; atom_nameatom_typeatom_chargecharge_group
>> >
>> > I have to specify the "atom name," force field "atom type," "atom
>> charge,"
>> > and "charge group" for every atom in the "TEST" residue in order. The
>> "atom
>> > name" must match the "atom name" in the input coordinate file but the
>> > mapping is applied by the entry order, correct? I do no need unique
>> "atom
>> > names," correct?
>> >
>> > Best,
>> > Eric
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 10/29/14 12:55 PM, Eric Smoll wrote:

Hi Mark,

Thanks for your help. I am looking for a deeper understanding "residue
names," "atom names," and how they are used to properly form input for
grompp.

By experimentation, it appears the pdb2gmx requires unique "atom names"
within each residue of the .rtp file to properly process .gro/.pdb files.
Thus, every "atom name" of a residue in the .gro/.pdb file must be unique.


This is correct.  There's no other way to process the input file otherwise, 
because neither atom order nor atom numbering can be assumed.  The only thing 
that should be reasonably foolproof is atom naming.  Internally, pdb2gmx then 
maps the names within the residues to numbers before writing out the processed 
coordinate file and topology.



It this not made clear in the .rtp section of the manual. It also appears
that the bond directive is required, not optional as shown in the example
in the .rtp section of the manual.



Strictly speaking, [bonds] is not a required directive.  One can specify 
single-atom .rtp entries (e.g. ions) that will not have bonds.  So making bonds 
mandatory breaks any case that may have, for instance, coordinated ions.  So a 
[bonds] directive is required only if the residue has bonds.  That's certainly 
the majority of cases, but it would be wrong to say the directive is mandatory.



However, if I build a system using an .itp file and the [ molecules ]
directive, the requirements are more flexible. Again, I observe that while
the "atoms names" of the gro and .itp files must match within a given
residue, they need not be unique. This is not made clear in the manual. It
seems (I hope) that matching is accomplished by the "nr" field of the
.top/,itp file and the "atom number" field of the .gro/.pdb file.



grompp does check for atom name matches as a sanity check.  It will complain if 
there are mismatches, which guard against a user preparing everything manually 
and then hosing the simulation by having a different order.  Indeed, there is no 
requirement that atom names be unique here, but order is essential since all 
remaining interactions (bonds, angles, etc) are based on atom number.


The atom number field is not the deciding factor.  It's matching the order of 
the names in coordinates vs. topology.  See the "check_atom_names()" function in 
grompp.c in the source code.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 10/29/14 12:55 PM, Eric Smoll wrote:

Hi Mark,

Thanks for your help. I am looking for a deeper understanding "residue
names," "atom names," and how they are used to properly form input for
grompp.

By experimentation, it appears the pdb2gmx requires unique "atom names"
within each residue of the .rtp file to properly process .gro/.pdb files.
Thus, every "atom name" of a residue in the .gro/.pdb file must be unique.


This is correct.  There's no other way to process the input file otherwise, 
because neither atom order nor atom numbering can be assumed.  The only thing 
that should be reasonably foolproof is atom naming.  Internally, pdb2gmx then 
maps the names within the residues to numbers before writing out the processed 
coordinate file and topology.



It this not made clear in the .rtp section of the manual. It also appears
that the bond directive is required, not optional as shown in the example
in the .rtp section of the manual.



Strictly speaking, [bonds] is not a required directive.  One can specify 
single-atom .rtp entries (e.g. ions) that will not have bonds.  So making bonds 
mandatory breaks any case that may have, for instance, coordinated ions.  So a 
[bonds] directive is required only if the residue has bonds.  That's certainly 
the majority of cases, but it would be wrong to say the directive is mandatory.



However, if I build a system using an .itp file and the [ molecules ]
directive, the requirements are more flexible. Again, I observe that while
the "atoms names" of the gro and .itp files must match within a given
residue, they need not be unique. This is not made clear in the manual. It
seems (I hope) that matching is accomplished by the "nr" field of the
.top/,itp file and the "atom number" field of the .gro/.pdb file.



grompp does check for atom name matches as a sanity check.  It will complain if 
there are mismatches, which guard against a user preparing everything manually 
and then hosing the simulation by having a different order.  Indeed, there is no 
requirement that atom names be unique here, but order is essential since all 
remaining interactions (bonds, angles, etc) are based on atom number.


The atom number field is not the deciding factor.  It's matching the order of 
the names in coordinates vs. topology.  See the "check_atom_names()" function in 
grompp.c in the source code.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pdb2gmx

[Saumyak Mukherjee]

Dear Lamm,

It is GROMACS-5.0.7. So you need to use "gmx pdb2gmx" command.

Best Wishes,
Saumyak

On 31 March 2017 at 11:55, Lamm Gro  wrote:

> Dear Gromacs users ,
>
> I have installed Gromacs by this way :
> http://www.gromacs.org/Documentation/Installation_
> Instructions_5.0#quick-and-dirty-installation
>
>
> every thing was fine and I could install the package completely .
> But now I can't find pdb2gmx command !
> Can you please let me know what the problem is ?
> I have updated cmake and fftw !
>
> Best,
> Saeed.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Peter Stern]

Is your first residue GLY-12?
If so you have exactly 368 residues in your protein: 12-379

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of ?farial 
tavakoli? ??
Sent: Thursday, July 20, 2017 3:07 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] pdb2gmx

Hello
 I want to create a .gro and .top file from my protein that contains 379 
aminoacids in it's .pdb file by using gromos96 54a7 force field:
pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and 
topology files are created , I see that message:
Start terminus GLY-12: GLY-NH3+
End terminus PRO-379: COO-
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 368 residues with 3856 atoms Making bonds...
Number of bonds was 3938, now 3933
Generating angles, dihedrals and pairs...
Before cleaning: 6090 pairs
Before cleaning: 8285 dihedrals
Making cmap torsions...There are 2746 dihedrals, 2028 impropers, 5756 angles
  6090 pairs, 3933 bonds and 0 virtual sites Total mass 
42175.307 a.m.u.
Total charge -0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.46#

Writing coordinate file...

Back Off! I just backed up HDAC2.gro to ./#HDAC2.gro.1#
        - PLEASE NOTE  You have successfully generated a 
topology from: HDAC2.pdb.
The Gromos54a7 force field and the spce water model are used.
        - ETON ESAELP 

However, i ignored this message and continued to use grompp gmx grompp -f 
em.mdp -c solv.gro -p topol.top -o ions.tpr

but faced to this message:
  gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29# Setting the LD random 
seed to -1863558486 Generated 168 of the 1653 non-bonded parameter combinations 
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet Analysing residue names:
There are:   368    Protein residues
There are: 11240  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 79005.00 Calculating 
fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 
0.114 0.114 0.114 Estimate for the relative computational load of the PME mesh 
part: 0.10 This run will generate roughly 3 Mb of data

Back Off! I just backed up ions.tpr to ./#ions.tpr.36#


Is there anyone to help me? Why pdb2gmx didnt consider all 379 amino acids of 
my protein and why GOMACS excluded 3 bonded neighours of the protein and 
SOL?and would you please tell what ' removing all charge groups because 
cutoff-scheme=Verlet ' means ? I t means the system is neutral ?

thanks in advanceFarial


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx

[Justin Lemkul]

On 1/15/14, 10:06 AM, jwill...@andrew.cmu.edu wrote:

Hello,

I was under the impression that pdb2gmx was supposed to referance the
force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem
to be for me.

To double check, I removed all force field parameters from forcefield.itp
and pdb2gmx still ran and got the same result as before.

How do I make pdb2gmx referance oplsaa.ff/forcefield.itp?



pdb2gmx doesn't do much of anything with forcefield.itp.  You tell it which 
force field you want to use, then it makes use of lots of files in that 
directory (see the manual for the list).  Most significant is the .rtp file. 
The #include statement for the force field is then simply written to the .top 
based on your selection.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Mark Abraham]

Hi,

These errors mean exactly what they say. There's a mismatch between your
structure file and the residue structure in the database. So you need to
look at them both and see what is wrong. Chapter 5 of the manual is your
friend.

Mark
On 19/03/2015 3:17 am, "RJ"  wrote:

> Dear gmx,
>
>
> I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even
> cleaned my crystal structure using Discovery studio/swissviewer which shows
> no error on it. I wonder, how do i rectify this problem ?
>
>
> WARNING: WARNING: Residue 1 named MET of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> WARNING: WARNING: Residue 366 named LEU of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 7060 pairs
>
>
> Residue 32681 named GLN of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 4/7/15 7:53 AM, Sneha Menon wrote:

Dear all,

I want to simulate a polymer - triphenylphosphine connected to a
polyethylene glycol polymer using the CHARMM36  forcefield. I obtained the
parameters of this polymer (resname TPP) using SwissParam. I added this
molecule to the forcefield by following all the steps mentioned in :
http://www.gromacs.org/Documentation/Hotos/Adding_a_Residue_to_a_Force_Field

I want to embed this polymer into a lipid bilayer. I first tried to make a
topology file for the polymer using :
*pdb2gmx -f file.pdb -o file.gro*

However, it showed up the following error:
Fatal error:
Residue 1 named TPP of a molecule in the input file was mapped
to an entry in the topology database, but the atom 16 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

I compared the .rtp file as well as the input .pdb file for any missing
atoms. I could not find any atoms missing or discrepancy in the
atom/residue naming. What else could be the problem?



You need to provide the relevant snippets of the .rtp and .pdb files.  Something 
is missing or mismatched, otherwise pdb2gmx would not complain.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Sotirios Dionysios I. Papadatos]

If I got it right I would suggest this. Try removing parts in your overall 
structure. 
For example let's say your system has 3 components water, ATP, TPO. Try 
removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try 
once again pdb2gmx. This will make the "troubled" part "visible". 
As for the error message, this comes up when you are trying to simulate a 
molecule that is not included in the default molecule entries. So you will have 
to include it manually. But when you know which part produces the error then it 
will be much easier. 


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Saman 
Shahriyari 
Sent: Sunday, July 5, 2015 10:06 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] pdb2gmx error

Dear Users
I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled 
structure holding ATP, water and TPO as hetero atoms. but I am faced with the 
following error. I checked all LUE residues (although I have got no residue 
with 28215089 number) and I found no missing atom N. I am really wondering what 
should be my next step. could you help me on this?
"Fatal error:Residue 28215089 named LEU of a molecule in the input file was 
mapped to an entry in the topology database, but the atom N used in an 
interaction of type improper in that entry is not found in the input file. 
Perhaps your atom and/or residue naming needs to be fixed."
Best regardsSaman
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 7/26/15 6:46 AM, faride badalkhani wrote:

Dear all,

could anybody help me at this error?


Fatal error:
atom N not found in buiding block 1AMC while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



Use -ter and select appropriately (probably "None" in the case of a polymer, 
provided you're following 
http://www.gromacs.org/Documentation/How-tos/Polymers).  If you don't specify 
terminal patching, pdb2gmx defaults to assuming you want protein-like N- and 
C-terminal termini.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx warning

[Justin Lemkul]

On 7/26/15 6:55 AM, faride badalkhani wrote:

Dear all,
I am performing a simulation on a plymeric structure, and I can exwcute
pdb2gmx command successfully but there are some warnings as follows:

Warning: Starting residue AMC1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue AMI2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue AMI3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue AMI4 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue AMI5 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further
warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.


How can I solve this problem?



It's not actually a problem; warnings and notes are informative ("hey user, 
check and make sure this is right!").  Errors are problems.


You've got a polymer that is not a known biomolecule.  pdb2gmx simply does this 
check to determine how to treat the molecule and make sure you're not mixing 
things strangely.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Mark Abraham]

Hi,

Is it terminal? Are there specbonds in play? What's the GROMACS version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey 
wrote:

> Hi everyone,
>
> I'm getting the following warning when I try to run pdb2gmx on my protein
> structure:
>
> WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was
> mapped to an entry in the topology database, but the atom H used in an
> interaction of type dihedral in that entry is not found in the input file.
> Perhaps your atom and/or residue naming needs to be fixed.
>
> This warning is only present when I use the AMBER03 forcefield, all other
> forcefields seem to work fine. I have tried this with both a structure
> without hydrogens as well as a structure with hydrogens added, both with
> and without the -ignh flag. I tried looking at the amber03 database files
> as well as the amber99sb-ildn database files (amber99sb-ildn works just
> fine), but I could not find any reason why this particular residue would be
> problematic. pdb2gmx does not find any problems with the other proline
> residues in the protein (which look identical), so I am puzzled as to
> what's causing this.
>
> The proline residue is:
> ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
>   N
> ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
>   C
> ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
>   C
> ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
>   C
> ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
>   C
> ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
>   C
> ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
>   O
>
> Does anyone know what's going on here?
>
> Thanks in advance!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Dries Van Rompaey]

Hi Mark,

This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.

Kind regards,
Dries


On 7 October 2015 at 20:56, Mark Abraham  wrote:

> Hi,
>
> Is it terminal? Are there specbonds in play? What's the GROMACS version?
> What's your pdb2gmx command line? :-)
>
> Mark
>
> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
> dries.vanromp...@gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I'm getting the following warning when I try to run pdb2gmx on my protein
> > structure:
> >
> > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file
> was
> > mapped to an entry in the topology database, but the atom H used in an
> > interaction of type dihedral in that entry is not found in the input
> file.
> > Perhaps your atom and/or residue naming needs to be fixed.
> >
> > This warning is only present when I use the AMBER03 forcefield, all other
> > forcefields seem to work fine. I have tried this with both a structure
> > without hydrogens as well as a structure with hydrogens added, both with
> > and without the -ignh flag. I tried looking at the amber03 database files
> > as well as the amber99sb-ildn database files (amber99sb-ildn works just
> > fine), but I could not find any reason why this particular residue would
> be
> > problematic. pdb2gmx does not find any problems with the other proline
> > residues in the protein (which look identical), so I am puzzled as to
> > what's causing this.
> >
> > The proline residue is:
> > ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
> >   N
> > ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
> >   C
> > ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
> >   C
> > ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
> >   C
> > ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
> >   C
> > ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
> >   C
> > ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
> >   O
> >
> > Does anyone know what's going on here?
> >
> > Thanks in advance!
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 10/7/15 3:01 PM, Dries Van Rompaey wrote:

Hi Mark,

This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.



Non-terminal proline does not have an amide H.  If your force field .rtp file 
claims to use such an atom used in a dihedral (which is what the error message 
tells you is happening), find out who altered the file and reprimand them :)


-Justin


Kind regards,
Dries


On 7 October 2015 at 20:56, Mark Abraham  wrote:


Hi,

Is it terminal? Are there specbonds in play? What's the GROMACS version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
dries.vanromp...@gmail.com>
wrote:


Hi everyone,

I'm getting the following warning when I try to run pdb2gmx on my protein
structure:

WARNING: WARNING: Residue 168 named PRO of a molecule in the input file

was

mapped to an entry in the topology database, but the atom H used in an
interaction of type dihedral in that entry is not found in the input

file.

Perhaps your atom and/or residue naming needs to be fixed.

This warning is only present when I use the AMBER03 forcefield, all other
forcefields seem to work fine. I have tried this with both a structure
without hydrogens as well as a structure with hydrogens added, both with
and without the -ignh flag. I tried looking at the amber03 database files
as well as the amber99sb-ildn database files (amber99sb-ildn works just
fine), but I could not find any reason why this particular residue would

be

problematic. pdb2gmx does not find any problems with the other proline
residues in the protein (which look identical), so I am puzzled as to
what's causing this.

The proline residue is:
ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
   N
ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
   C
ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
   C
ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
   C
ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
   C
ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
   C
ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
   O

Does anyone know what's going on here?

Thanks in advance!
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Dries Van Rompaey]

Thanks Justin, that makes sense! I'm wondering why none of the other
proline residues triggered that warning though? The same procedure works
like a charm with other proteins.
On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:

>
>
> On 10/7/15 3:01 PM, Dries Van Rompaey wrote:
>
>> Hi Mark,
>>
>> This is Gromacs 5.0.4. This is a non-terminal residue.
>> The command line used is:
>> gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
>> I tried this procedure with and without ignh flag.
>> As far as I know, specbonds is not in play.
>>
>>
> Non-terminal proline does not have an amide H.  If your force field .rtp
> file claims to use such an atom used in a dihedral (which is what the error
> message tells you is happening), find out who altered the file and
> reprimand them :)
>
> -Justin
>
> Kind regards,
>> Dries
>>
>>
>> On 7 October 2015 at 20:56, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> Is it terminal? Are there specbonds in play? What's the GROMACS version?
>>> What's your pdb2gmx command line? :-)
>>>
>>> Mark
>>>
>>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
>>> dries.vanromp...@gmail.com>
>>> wrote:
>>>
>>> Hi everyone,

 I'm getting the following warning when I try to run pdb2gmx on my
 protein
 structure:

 WARNING: WARNING: Residue 168 named PRO of a molecule in the input file

>>> was
>>>
 mapped to an entry in the topology database, but the atom H used in an
 interaction of type dihedral in that entry is not found in the input

>>> file.
>>>
 Perhaps your atom and/or residue naming needs to be fixed.

 This warning is only present when I use the AMBER03 forcefield, all
 other
 forcefields seem to work fine. I have tried this with both a structure
 without hydrogens as well as a structure with hydrogens added, both with
 and without the -ignh flag. I tried looking at the amber03 database
 files
 as well as the amber99sb-ildn database files (amber99sb-ildn works just
 fine), but I could not find any reason why this particular residue would

>>> be
>>>
 problematic. pdb2gmx does not find any problems with the other proline
 residues in the protein (which look identical), so I am puzzled as to
 what's causing this.

 The proline residue is:
 ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
N
 ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
C
 ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
C
 ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
C
 ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
C
 ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
C
 ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
O

 Does anyone know what's going on here?

 Thanks in advance!
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

 --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 10/7/15 5:03 PM, Dries Van Rompaey wrote:

Thanks Justin, that makes sense! I'm wondering why none of the other
proline residues triggered that warning though? The same procedure works
like a charm with other proteins.


Without access to all of the files you're looking at, the best I can do is shrug 
my shoulders because that doesn't make any sense.  Some prolines work and one 
doesn't?  That's just not logical.


-Justin


On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:




On 10/7/15 3:01 PM, Dries Van Rompaey wrote:


Hi Mark,

This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.



Non-terminal proline does not have an amide H.  If your force field .rtp
file claims to use such an atom used in a dihedral (which is what the error
message tells you is happening), find out who altered the file and
reprimand them :)

-Justin

Kind regards,

Dries


On 7 October 2015 at 20:56, Mark Abraham 
wrote:

Hi,


Is it terminal? Are there specbonds in play? What's the GROMACS version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
dries.vanromp...@gmail.com>
wrote:

Hi everyone,


I'm getting the following warning when I try to run pdb2gmx on my
protein
structure:

WARNING: WARNING: Residue 168 named PRO of a molecule in the input file


was


mapped to an entry in the topology database, but the atom H used in an
interaction of type dihedral in that entry is not found in the input


file.


Perhaps your atom and/or residue naming needs to be fixed.

This warning is only present when I use the AMBER03 forcefield, all
other
forcefields seem to work fine. I have tried this with both a structure
without hydrogens as well as a structure with hydrogens added, both with
and without the -ignh flag. I tried looking at the amber03 database
files
as well as the amber99sb-ildn database files (amber99sb-ildn works just
fine), but I could not find any reason why this particular residue would


be


problematic. pdb2gmx does not find any problems with the other proline
residues in the protein (which look identical), so I am puzzled as to
what's causing this.

The proline residue is:
ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
N
ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
C
ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
C
ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
C
ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
C
ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
C
ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
O

Does anyone know what's going on here?

Thanks in advance!
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.

--

Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.

Re: [gmx-users] pdb2gmx error

[Dries Van Rompaey]

Thanks for the reply Justin. I unfortunately cannot currently disclose the
files that I'm working on. Based on the info presented, would you say that
it's an issue with the force field definition or with the actual protein
topology? I am not planning on using amber03 in my simulations at the
moment, so this specific warning is not that important, but I can't help
but wonder if this warning means something is off in the topology.

On 7 October 2015 at 23:05, Justin Lemkul  wrote:

>
>
> On 10/7/15 5:03 PM, Dries Van Rompaey wrote:
>
>> Thanks Justin, that makes sense! I'm wondering why none of the other
>> proline residues triggered that warning though? The same procedure works
>> like a charm with other proteins.
>>
>
> Without access to all of the files you're looking at, the best I can do is
> shrug my shoulders because that doesn't make any sense.  Some prolines work
> and one doesn't?  That's just not logical.
>
> -Justin
>
>
> On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:
>>
>>
>>>
>>> On 10/7/15 3:01 PM, Dries Van Rompaey wrote:
>>>
>>> Hi Mark,

 This is Gromacs 5.0.4. This is a non-terminal residue.
 The command line used is:
 gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
 I tried this procedure with and without ignh flag.
 As far as I know, specbonds is not in play.


 Non-terminal proline does not have an amide H.  If your force field .rtp
>>> file claims to use such an atom used in a dihedral (which is what the
>>> error
>>> message tells you is happening), find out who altered the file and
>>> reprimand them :)
>>>
>>> -Justin
>>>
>>> Kind regards,
>>>
 Dries


 On 7 October 2015 at 20:56, Mark Abraham 
 wrote:

 Hi,

>
> Is it terminal? Are there specbonds in play? What's the GROMACS
> version?
> What's your pdb2gmx command line? :-)
>
> Mark
>
> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
> dries.vanromp...@gmail.com>
> wrote:
>
> Hi everyone,
>
>>
>> I'm getting the following warning when I try to run pdb2gmx on my
>> protein
>> structure:
>>
>> WARNING: WARNING: Residue 168 named PRO of a molecule in the input
>> file
>>
>> was
>
> mapped to an entry in the topology database, but the atom H used in an
>> interaction of type dihedral in that entry is not found in the input
>>
>> file.
>
> Perhaps your atom and/or residue naming needs to be fixed.
>>
>> This warning is only present when I use the AMBER03 forcefield, all
>> other
>> forcefields seem to work fine. I have tried this with both a structure
>> without hydrogens as well as a structure with hydrogens added, both
>> with
>> and without the -ignh flag. I tried looking at the amber03 database
>> files
>> as well as the amber99sb-ildn database files (amber99sb-ildn works
>> just
>> fine), but I could not find any reason why this particular residue
>> would
>>
>> be
>
> problematic. pdb2gmx does not find any problems with the other proline
>> residues in the protein (which look identical), so I am puzzled as to
>> what's causing this.
>>
>> The proline residue is:
>> ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
>> N
>> ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
>> C
>> ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
>> C
>> ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
>> C
>> ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
>> C
>> ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
>> C
>> ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
>> O
>>
>> Does anyone know what's going on here?
>>
>> Thanks in advance!
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>> --
>>
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> D

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 10/8/15 1:54 AM, Dries Van Rompaey wrote:

Thanks for the reply Justin. I unfortunately cannot currently disclose the
files that I'm working on. Based on the info presented, would you say that
it's an issue with the force field definition or with the actual protein
topology? I am not planning on using amber03 in my simulations at the
moment, so this specific warning is not that important, but I can't help
but wonder if this warning means something is off in the topology.



Given that error, there is no topology produced, so there's not going to be a 
problem with the topology itself.


I'm sorry to say that without your actual files, there's literally nothing we 
can do to diagnose this.  You say some prolines work with AMBER03 and others 
don't, which makes no sense at all.  Either the .rtp is sound or it isn't. 
Either it is unmodified (which will work) or someone has tampered with it and 
broken it.


If you're not going to use AMBER03 and the topology is produced with other force 
fields, then you know you have a problem with a hacked AMBER03 .rtp file.  It 
should be very straightforward to simply to a diff against the unmodified 
version (which you can get by downloading a fresh GROMACS tarball if you don't 
already have it).


-Justin


On 7 October 2015 at 23:05, Justin Lemkul  wrote:




On 10/7/15 5:03 PM, Dries Van Rompaey wrote:


Thanks Justin, that makes sense! I'm wondering why none of the other
proline residues triggered that warning though? The same procedure works
like a charm with other proteins.



Without access to all of the files you're looking at, the best I can do is
shrug my shoulders because that doesn't make any sense.  Some prolines work
and one doesn't?  That's just not logical.

-Justin


On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:





On 10/7/15 3:01 PM, Dries Van Rompaey wrote:

Hi Mark,


This is Gromacs 5.0.4. This is a non-terminal residue.
The command line used is:
gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
I tried this procedure with and without ignh flag.
As far as I know, specbonds is not in play.


Non-terminal proline does not have an amide H.  If your force field .rtp

file claims to use such an atom used in a dihedral (which is what the
error
message tells you is happening), find out who altered the file and
reprimand them :)

-Justin

Kind regards,


Dries


On 7 October 2015 at 20:56, Mark Abraham 
wrote:

Hi,



Is it terminal? Are there specbonds in play? What's the GROMACS
version?
What's your pdb2gmx command line? :-)

Mark

On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
dries.vanromp...@gmail.com>
wrote:

Hi everyone,



I'm getting the following warning when I try to run pdb2gmx on my
protein
structure:

WARNING: WARNING: Residue 168 named PRO of a molecule in the input
file

was


mapped to an entry in the topology database, but the atom H used in an

interaction of type dihedral in that entry is not found in the input

file.


Perhaps your atom and/or residue naming needs to be fixed.


This warning is only present when I use the AMBER03 forcefield, all
other
forcefields seem to work fine. I have tried this with both a structure
without hydrogens as well as a structure with hydrogens added, both
with
and without the -ignh flag. I tried looking at the amber03 database
files
as well as the amber99sb-ildn database files (amber99sb-ildn works
just
fine), but I could not find any reason why this particular residue
would

be


problematic. pdb2gmx does not find any problems with the other proline

residues in the protein (which look identical), so I am puzzled as to
what's causing this.

The proline residue is:
ATOM   1384  N   PRO A 168 274.650  45.241  24.167  1.00180.63
 N
ATOM   1385  CA  PRO A 168 273.508  44.823  23.370  1.00180.63
 C
ATOM   1386  CD  PRO A 168 275.844  45.381  23.346  1.00180.63
 C
ATOM   1387  CB  PRO A 168 274.071  44.405  22.014  1.00180.63
 C
ATOM   1388  CG  PRO A 168 275.381  45.194  21.892  1.00180.63
 C
ATOM   1389  C   PRO A 168 272.551  43.776  23.888  1.00180.63
 C
ATOM   1390  O   PRO A 168 271.478  43.646  23.304  1.00180.63
 O

Does anyone know what's going on here?

Thanks in advance!
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.

--


Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--

==

Ju

Re: [gmx-users] pdb2gmx error

[Dries Van Rompaey]

I definitely agree that it's odd that the warning only occurs with this
specific residue. I ran a diff against the freshly downloaded AMBER03
files, but they were identical. I also tried running it again with freshly
downloaded amber03 files in the directory.

About the error: pdb2gmx never crashed. It always runs to completion and
mentions that the topology was successfully generated. I only get a warning
during the execution of pdb2gmx.

Thanks for all your help,

Dries



On 8 October 2015 at 13:33, Justin Lemkul  wrote:

>
>
> On 10/8/15 1:54 AM, Dries Van Rompaey wrote:
>
>> Thanks for the reply Justin. I unfortunately cannot currently disclose the
>> files that I'm working on. Based on the info presented, would you say that
>> it's an issue with the force field definition or with the actual protein
>> topology? I am not planning on using amber03 in my simulations at the
>> moment, so this specific warning is not that important, but I can't help
>> but wonder if this warning means something is off in the topology.
>>
>>
> Given that error, there is no topology produced, so there's not going to
> be a problem with the topology itself.
>
> I'm sorry to say that without your actual files, there's literally nothing
> we can do to diagnose this.  You say some prolines work with AMBER03 and
> others don't, which makes no sense at all.  Either the .rtp is sound or it
> isn't. Either it is unmodified (which will work) or someone has tampered
> with it and broken it.
>
> If you're not going to use AMBER03 and the topology is produced with other
> force fields, then you know you have a problem with a hacked AMBER03 .rtp
> file.  It should be very straightforward to simply to a diff against the
> unmodified version (which you can get by downloading a fresh GROMACS
> tarball if you don't already have it).
>
> -Justin
>
>
> On 7 October 2015 at 23:05, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/7/15 5:03 PM, Dries Van Rompaey wrote:
>>>
>>> Thanks Justin, that makes sense! I'm wondering why none of the other
 proline residues triggered that warning though? The same procedure works
 like a charm with other proteins.


>>> Without access to all of the files you're looking at, the best I can do
>>> is
>>> shrug my shoulders because that doesn't make any sense.  Some prolines
>>> work
>>> and one doesn't?  That's just not logical.
>>>
>>> -Justin
>>>
>>>
>>> On 7 Oct 2015 10:59 pm, "Justin Lemkul"  wrote:
>>>



> On 10/7/15 3:01 PM, Dries Van Rompaey wrote:
>
> Hi Mark,
>
>>
>> This is Gromacs 5.0.4. This is a non-terminal residue.
>> The command line used is:
>> gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh)
>> I tried this procedure with and without ignh flag.
>> As far as I know, specbonds is not in play.
>>
>>
>> Non-terminal proline does not have an amide H.  If your force field
>> .rtp
>>
> file claims to use such an atom used in a dihedral (which is what the
> error
> message tells you is happening), find out who altered the file and
> reprimand them :)
>
> -Justin
>
> Kind regards,
>
> Dries
>>
>>
>> On 7 October 2015 at 20:56, Mark Abraham 
>> wrote:
>>
>> Hi,
>>
>>
>>> Is it terminal? Are there specbonds in play? What's the GROMACS
>>> version?
>>> What's your pdb2gmx command line? :-)
>>>
>>> Mark
>>>
>>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey <
>>> dries.vanromp...@gmail.com>
>>> wrote:
>>>
>>> Hi everyone,
>>>
>>>
 I'm getting the following warning when I try to run pdb2gmx on my
 protein
 structure:

 WARNING: WARNING: Residue 168 named PRO of a molecule in the input
 file

 was

>>>
>>> mapped to an entry in the topology database, but the atom H used in
>>> an
>>>
 interaction of type dihedral in that entry is not found in the input

 file.

>>>
>>> Perhaps your atom and/or residue naming needs to be fixed.
>>>

 This warning is only present when I use the AMBER03 forcefield, all
 other
 forcefields seem to work fine. I have tried this with both a
 structure
 without hydrogens as well as a structure with hydrogens added, both
 with
 and without the -ignh flag. I tried looking at the amber03 database
 files
 as well as the amber99sb-ildn database files (amber99sb-ildn works
 just
 fine), but I could not find any reason why this particular residue
 would

 be

>>>
>>> problematic. pdb2gmx does not find any problems with the other
>>> proline
>>>
 residues in the protein (which look identical), so I am puzzled as
 to
 what's causing this.

 The proline residue is:
 ATO

Re: [gmx-users] pdb2gmx error

[Dries Van Rompaey]

I did some more testing, it seems that this only occurs when the PRO
residue is preceded by a glycine. Could this be related to this issue:
http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I
change the glycine residue to anything else, pdb2gmx works like a charm. I
constructed a simple test system in which I can replicate the error (see
below).


REMARK  99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39
2015
ATOM  1  N   ALA 1   0.268  -1.146  -1.547  1.00  0.00
  N1+
ATOM  2  CA  ALA 1   0.506   0.327  -1.714  1.00  0.00
  C
ATOM  3  CB  ALA 1  -0.837   1.004  -1.931  1.00  0.00
  C
ATOM  4  C   ALA 1   1.226   0.877  -0.480  1.00  0.00
  C
ATOM  5  O   ALA 1   1.399   0.165   0.509  1.00  0.00
  O
ATOM  6  H1  ALA 1  -0.272  -1.324  -0.688  1.00  0.00
  H
ATOM  7  H2  ALA 1  -0.224  -1.571  -2.343  1.00  0.00
  H
ATOM  8  H3  ALA 1   1.161  -1.641  -1.413  1.00  0.00
  H
ATOM  9  HA  ALA 1   1.151   0.435  -2.592  1.00  0.00
  H
ATOM 10  HB1 ALA 1  -1.364   0.570  -2.788  1.00  0.00
  H
ATOM 11  HB2 ALA 1  -1.480   0.906  -1.049  1.00  0.00
  H
ATOM 12  HB3 ALA 1  -0.710   2.074  -2.125  1.00  0.00
  H
ATOM 13  N   GLY 2   1.667   2.171  -0.583  1.00  0.00
  N
ATOM 14  CA  GLY 2   2.390   2.835   0.493  1.00  0.00
  C
ATOM 15  C   GLY 2   2.792   4.221   0.005  1.00  0.00
  C
ATOM 16  O   GLY 2   2.258   4.706  -0.997  1.00  0.00
  O
ATOM 17  H   GLY 2   1.519   2.744  -1.415  1.00  0.00
  H
ATOM 18  HA1 GLY 2   1.730   2.918   1.361  1.00  0.00
  H
ATOM 19  HA2 GLY 2   3.269   2.234   0.743  1.00  0.00
  H
ATOM 20  N   PRO 3   3.764   4.872   0.730  1.00  0.00
  N
ATOM 21  CD  PRO 3   4.331   4.472   2.006  1.00  0.00
  C
ATOM 22  CG  PRO 3   4.793   5.786   2.610  1.00  0.00
  C
ATOM 23  CB  PRO 3   5.270   6.581   1.399  1.00  0.00
  C
ATOM 24  CA  PRO 3   4.347   6.129   0.260  1.00  0.00
  C
ATOM 25  C   PRO 3   5.168   5.908  -1.021  1.00  0.00
  C
ATOM 26  O   PRO 3   5.520   4.796  -1.412  1.00  0.00
  O
ATOM 27  HA  PRO 3   3.538   6.843   0.069  1.00  0.00
  H
ATOM 28  HB1 PRO 3   6.318   6.337   1.188  1.00  0.00
  H
ATOM 29  HB2 PRO 3   5.212   7.661   1.568  1.00  0.00
  H
ATOM 30  HG1 PRO 3   5.571   5.654   3.367  1.00  0.00
  H
ATOM 31  HG2 PRO 3   3.945   6.303   3.076  1.00  0.00
  H
ATOM 32  HD1 PRO 3   5.175   3.804   1.803  1.00  0.00
  H
ATOM 33  HD2 PRO 3   3.599   3.952   2.629  1.00  0.00
  H
ATOM 34  N   ALA 4   5.499   7.083  -1.656  1.00  0.00
  N
ATOM 35  CA  ALA 4   6.262   7.165  -2.905  1.00  0.00
  C
ATOM 36  CB  ALA 4   5.416   6.725  -4.094  1.00  0.00
  C
ATOM 37  C   ALA 4   6.738   8.618  -3.177  1.00  0.00
  C
ATOM 38  OXT ALA 4   7.513   8.768  -4.161  1.00  0.00
  O1-
ATOM 39  O   ALA 4   6.290   9.477  -2.354  1.00  0.00
  O
ATOM 40  H   ALA 4   5.250   8.002  -1.288  1.00  0.00
  H
ATOM 41  HA  ALA 4   7.137   6.512  -2.806  1.00  0.00
  H
ATOM 42  HB1 ALA 4   4.539   7.372  -4.215  1.00  0.00
  H
ATOM 43  HB2 ALA 4   5.988   6.759  -5.027  1.00  0.00
  H
ATOM 44  HB3 ALA 4   5.053   5.700  -3.965  1.00  0.00
  H
TER  45  ALA 4
END


On 8 October 2015 at 14:15, Dries Van Rompaey 
wrote:

> I definitely agree that it's odd that the warning only occurs with this
> specific residue. I ran a diff against the freshly downloaded AMBER03
> files, but they were identical. I also tried running it again with freshly
> downloaded amber03 files in the directory.
>
> About the error: pdb2gmx never crashed. It always runs to completion and
> mentions that the topology was successfully generated. I only get a warning
> during the execution of pdb2gmx.
>
> Thanks for all your help,
>
> Dries
>
>
>
> On 8 October 2015 at 13:33, Justin Lemkul  wrote:
>
>>
>>
>> On 10/8/15 1:54 AM, Dries Van Rompaey wrote:
>>
>>> Thanks for the reply Justin. I unfortunately cannot currently disclose
>>> the
>>> files that I'm working on. Based on the info presented, would you say
>>> that
>>> it's an issue with the force field definition or with the actual protein
>>> topology? I am not planning on using amber03 in my simulations at the
>>> moment, so this specific warning is not that important, but I can't help
>>> but wonder if this warning means something is off in the topology.
>>>
>>>
>> Given that error, there is no topology produced, so there's not going to
>> be a problem with the topology itself.
>>
>> I'm sorry to say that without your actual files, there's literally
>> nothing we can do to diagnose this.  You say s

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 10/15/15 4:18 AM, Dries Van Rompaey wrote:

I did some more testing, it seems that this only occurs when the PRO
residue is preceded by a glycine. Could this be related to this issue:
http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I
change the glycine residue to anything else, pdb2gmx works like a charm. I
constructed a simple test system in which I can replicate the error (see
below).



Indeed, it seems that the AMBER03 version of GLY has a bunch of dihedrals 
defined that shouldn't be.  It also looks like it is the only AMBER force field 
that does this, so it's clearly a mistake.  I will submit a patch for the 5.1 
series.  Thanks for digging into this.


-Justin



REMARK  99 MOE v2014.09 (Chemical Computing Group Inc.) Thu Oct 15 10:05:39
2015
ATOM  1  N   ALA 1   0.268  -1.146  -1.547  1.00  0.00
   N1+
ATOM  2  CA  ALA 1   0.506   0.327  -1.714  1.00  0.00
   C
ATOM  3  CB  ALA 1  -0.837   1.004  -1.931  1.00  0.00
   C
ATOM  4  C   ALA 1   1.226   0.877  -0.480  1.00  0.00
   C
ATOM  5  O   ALA 1   1.399   0.165   0.509  1.00  0.00
   O
ATOM  6  H1  ALA 1  -0.272  -1.324  -0.688  1.00  0.00
   H
ATOM  7  H2  ALA 1  -0.224  -1.571  -2.343  1.00  0.00
   H
ATOM  8  H3  ALA 1   1.161  -1.641  -1.413  1.00  0.00
   H
ATOM  9  HA  ALA 1   1.151   0.435  -2.592  1.00  0.00
   H
ATOM 10  HB1 ALA 1  -1.364   0.570  -2.788  1.00  0.00
   H
ATOM 11  HB2 ALA 1  -1.480   0.906  -1.049  1.00  0.00
   H
ATOM 12  HB3 ALA 1  -0.710   2.074  -2.125  1.00  0.00
   H
ATOM 13  N   GLY 2   1.667   2.171  -0.583  1.00  0.00
   N
ATOM 14  CA  GLY 2   2.390   2.835   0.493  1.00  0.00
   C
ATOM 15  C   GLY 2   2.792   4.221   0.005  1.00  0.00
   C
ATOM 16  O   GLY 2   2.258   4.706  -0.997  1.00  0.00
   O
ATOM 17  H   GLY 2   1.519   2.744  -1.415  1.00  0.00
   H
ATOM 18  HA1 GLY 2   1.730   2.918   1.361  1.00  0.00
   H
ATOM 19  HA2 GLY 2   3.269   2.234   0.743  1.00  0.00
   H
ATOM 20  N   PRO 3   3.764   4.872   0.730  1.00  0.00
   N
ATOM 21  CD  PRO 3   4.331   4.472   2.006  1.00  0.00
   C
ATOM 22  CG  PRO 3   4.793   5.786   2.610  1.00  0.00
   C
ATOM 23  CB  PRO 3   5.270   6.581   1.399  1.00  0.00
   C
ATOM 24  CA  PRO 3   4.347   6.129   0.260  1.00  0.00
   C
ATOM 25  C   PRO 3   5.168   5.908  -1.021  1.00  0.00
   C
ATOM 26  O   PRO 3   5.520   4.796  -1.412  1.00  0.00
   O
ATOM 27  HA  PRO 3   3.538   6.843   0.069  1.00  0.00
   H
ATOM 28  HB1 PRO 3   6.318   6.337   1.188  1.00  0.00
   H
ATOM 29  HB2 PRO 3   5.212   7.661   1.568  1.00  0.00
   H
ATOM 30  HG1 PRO 3   5.571   5.654   3.367  1.00  0.00
   H
ATOM 31  HG2 PRO 3   3.945   6.303   3.076  1.00  0.00
   H
ATOM 32  HD1 PRO 3   5.175   3.804   1.803  1.00  0.00
   H
ATOM 33  HD2 PRO 3   3.599   3.952   2.629  1.00  0.00
   H
ATOM 34  N   ALA 4   5.499   7.083  -1.656  1.00  0.00
   N
ATOM 35  CA  ALA 4   6.262   7.165  -2.905  1.00  0.00
   C
ATOM 36  CB  ALA 4   5.416   6.725  -4.094  1.00  0.00
   C
ATOM 37  C   ALA 4   6.738   8.618  -3.177  1.00  0.00
   C
ATOM 38  OXT ALA 4   7.513   8.768  -4.161  1.00  0.00
   O1-
ATOM 39  O   ALA 4   6.290   9.477  -2.354  1.00  0.00
   O
ATOM 40  H   ALA 4   5.250   8.002  -1.288  1.00  0.00
   H
ATOM 41  HA  ALA 4   7.137   6.512  -2.806  1.00  0.00
   H
ATOM 42  HB1 ALA 4   4.539   7.372  -4.215  1.00  0.00
   H
ATOM 43  HB2 ALA 4   5.988   6.759  -5.027  1.00  0.00
   H
ATOM 44  HB3 ALA 4   5.053   5.700  -3.965  1.00  0.00
   H
TER  45  ALA 4
END


On 8 October 2015 at 14:15, Dries Van Rompaey 
wrote:


I definitely agree that it's odd that the warning only occurs with this
specific residue. I ran a diff against the freshly downloaded AMBER03
files, but they were identical. I also tried running it again with freshly
downloaded amber03 files in the directory.

About the error: pdb2gmx never crashed. It always runs to completion and
mentions that the topology was successfully generated. I only get a warning
during the execution of pdb2gmx.

Thanks for all your help,

Dries



On 8 October 2015 at 13:33, Justin Lemkul  wrote:




On 10/8/15 1:54 AM, Dries Van Rompaey wrote:


Thanks for the reply Justin. I unfortunately cannot currently disclose
the
files that I'm working on. Based on the info presented, would you say
that
it's an issue with the force field definition or with the actual protein
topology? I am not planning on using amber03 in my simulations at the
moment, so this specific warning is not that important, but I can't hel

Re: [gmx-users] pdb2gmx error

[Justin Lemkul]

On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote:

Hello,

When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force 
field, I have the error :
Fatal error:
tpA = 53191, i= 0 in print_atoms

I have no idea what does this message mean. Could you help me?



This shouldn't happen.  Have you or anyone else modified the code or force field 
files?  That's the only instance in which this would be triggered.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[ABEL Stephane 175950]

Indeed Justin I have tried to add  the entries for the capped groups in the 
Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present 
in  aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken 
something 

Stéphane


On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote:
> Hello,
>
> When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN 
> force field, I have the error :
> Fatal error:
> tpA = 53191, i= 0 in print_atoms
>
> I have no idea what does this message mean. Could you help me?
>

This shouldn't happen.  Have you or anyone else modified the code or force field
files?  That's the only instance in which this would be triggered.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==

***
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx -ignh

[Justin Lemkul]

On 5/4/16 5:02 AM, Alexander Alexander wrote:

Dear GMX user,

As you know, naming the Hydrogen atom differently in different FF and in
.pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met
the issue when I wanted to convert my self-made (by Avogadro)
heptapeptide.pdb to heptapeptide.gro file.

I could get rid of them using "-ignh" which is ignoring H atom in the
heptapeptide.pdb file.Then, If I understood correctly this means no normal
Hydrogen atom there is in produced heptapeptide.gro file?! If so, do you
think if this makes sense proceed further with a peptide which is missing
the normal hydrogen atom in?



-ignh does not mean that there are no H in the output, only that H in the input 
are ignored.  pdb2gmx reconstructs missing H using .hdb entries.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error

[bharat gupta]

Hi,

I have been trying to build the toplogy for cellopentoase using the newly
derived parameters mentioned in this paper:
http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the
gromacs website:
http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar

When I try to construct the topology file using this forcefield, I am
getting the following error:

Fatal error:
Residue 6 named GLCN of a molecule in the input file was mapped
to an entry in the topology database, but the atom C1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

I have only 5 residues in the pdb file, but gromacs is counting it as 6
residues. Here's the pdb file:

HEADER CP5
ATOM  1  O2  GLC01   7.400   0.776  35.278  0.70 24.55
  O
ATOM  2  C2  GLC01   6.024   0.721  35.632  0.70 23.65
  C
ATOM  3  C3  GLC01   5.240   0.984  34.354  0.70 21.57
  C
ATOM  4  O3  GLC01   5.144  -0.245  33.608  0.70 14.59
  O
ATOM  5  C4  GLC01   3.902   1.571  34.776  0.70 20.91
  C
ATOM  6  O4  GLC01   3.006   1.662  33.670  0.70 19.67
  O
ATOM  7  C5  GLC01   4.174   2.944  35.391  0.70 22.32
  C
ATOM  8  C6  GLC01   2.914   3.605  35.899  0.70 21.51
  C
ATOM  9  O6  GLC01   2.201   2.690  36.737  0.70 20.09
  O
ATOM 10  O5  GLC01   5.080   2.890  36.510  0.70 24.12
  O
ATOM 11  C1  GLC01   5.742   1.651  36.843  0.70 26.75
  C
ATOM 12  O1  GLC 1   5.207   0.892  37.971  0.70 30.32
  O
ATOM 13  C4  GLC 2   4.222   1.340  38.917  0.70 32.87
  C
ATOM 14  C5  GLC 2   4.753   1.239  40.352  0.70 33.51
  C
ATOM 15  O5  GLC 2   3.711   1.506  41.306  0.70 35.29
  O
ATOM 16  C6  GLC 2   5.888   2.194  40.665  0.70 34.02
  C
ATOM 17  O6  GLC 2   5.803   2.537  42.057  0.70 32.97
  O
ATOM 18  C3  GLC 2   3.072   0.331  38.851  0.70 33.72
  C
ATOM 19  O3  GLC 2   2.435   0.360  37.564  0.70 34.01
  O
ATOM 20  C2  GLC 2   2.027   0.450  39.972  0.70 35.29
  C
ATOM 21  O2  GLC 2   1.149  -0.684  39.932  0.70 36.32
  O
ATOM 22  C1  GLC 2   2.684   0.512  41.351  0.70 36.04
  C
ATOM 23  O1  GLC 2   1.704   0.843  42.349  0.70 36.96
  O
ATOM 24  C4  GLC 3   2.032   0.454  43.689  0.70 38.12
  C
ATOM 25  C5  GLC 3   0.810  -0.195  44.344  0.70 38.87
  C
ATOM 26  O5  GLC 3   1.085  -0.507  45.715  0.70 39.40
  O
ATOM 27  C6  GLC 3   0.372  -1.455  43.605  0.70 38.87
  C
ATOM 28  O6  GLC 3  -0.996  -1.300  43.220  0.70 39.09
  O
ATOM 29  C3  GLC 3   2.455   1.683  44.498  0.70 38.55
  C
ATOM 30  O3  GLC 3   3.729   2.152  44.043  0.70 38.93
  O
ATOM 31  C2  GLC 3   2.550   1.405  45.997  0.70 39.25
  C
ATOM 32  O2  GLC 3   2.700   2.646  46.700  0.70 38.44
  O
ATOM 33  C1  GLC 3   1.319   0.663  46.514  0.70 39.97
  C
ATOM 34  O1  GLC 3   1.522   0.333  47.897  0.70 41.30
  O
ATOM 35  C4  GLC 4   0.320  -0.039  48.583  0.70 42.19
  C
ATOM 36  C5  GLC 4  -0.067   0.972  49.664  0.70 42.80
  C
ATOM 37  O5  GLC 4  -1.358   0.617  50.163  0.70 43.08
  O
ATOM 38  C6  GLC 4  -0.082   2.420  49.189  0.70 43.23
  C
ATOM 39  O6  GLC 4  -0.900   2.532  48.019  0.70 43.36
  O
ATOM 40  C3  GLC 4   0.485  -1.387  49.281  0.70 42.24
  C
ATOM 41  O3  GLC 4   0.818  -2.397  48.323  0.70 41.16
  O
ATOM 42  C2  GLC 4  -0.782  -1.783  50.046  0.70 42.64
  C
ATOM 43  O2  GLC 4  -0.470  -2.862  50.935  0.70 42.32
  O
ATOM 44  C1  GLC 4  -1.375  -0.633  50.870  0.70 43.60
  C
ATOM 45  O1  GLCN4  -2.732  -0.947  51.190  0.70 45.14
  O
ATOM 46  C4  GLCN5  -3.137  -0.484  52.482  0.70 46.29
  C
ATOM 47  C3  GLCN5  -4.035   0.750  52.337  0.70 46.70
  C
ATOM 48  O3  GLCN5  -3.269   1.864  51.865  0.70 46.85
  O
ATOM 49  C2  GLCN5  -4.706   1.124  53.659  0.70 47.10
  C
ATOM 50  O2  GLCN5  -5.680   2.147  53.435  0.70 47.17
  O
ATOM 51  C1  GLCN5  -5.377  -0.097  54.282  0.70 47.34
  C
ATOM 52  O1  GLCN5  -5.958   0.264  55.539  0.70 47.48
  O
ATOM 53  O5  GLCN5  -4.397  -1.126  54.467  0.70 47.17
  O
ATOM 54  C5  GLCN5  -3.867  -1.611  53.225  0.70 46.80
  C
ATOM 55  C6  GLCN5  -2.967  -2.814  53.497  0.70 46.93
  C
ATOM 56  O6  GLCN5  -1.934  -2.454  54.421  0.70 47.39
  O
END

Can anyone let me know what am I doing wrong?

I am trying to perform MD simulation of protein with cellopentoase. So, in
order to obtain the parameters for cellopentoase, I am following the
parameters mentioned above.


-- 
*Best Regards*
Bharat
-- 
Gromacs Users mailing list

* Ple

Re: [gmx-users] pdb2gmx error

[Mark Abraham]

Hi,

Why is your residue numbering and residue naming changing in mutually
inconsistent ways?

Mark

On Thu, Jun 16, 2016 at 9:36 AM bharat gupta 
wrote:

> Hi,
>
> I have been trying to build the toplogy for cellopentoase using the newly
> derived parameters mentioned in this paper:
> http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the
> gromacs website:
> http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar
>
> When I try to construct the topology file using this forcefield, I am
> getting the following error:
>
> Fatal error:
> Residue 6 named GLCN of a molecule in the input file was mapped
> to an entry in the topology database, but the atom C1 used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
>
> I have only 5 residues in the pdb file, but gromacs is counting it as 6
> residues. Here's the pdb file:
>
> HEADER CP5
> ATOM  1  O2  GLC01   7.400   0.776  35.278  0.70 24.55
>   O
> ATOM  2  C2  GLC01   6.024   0.721  35.632  0.70 23.65
>   C
> ATOM  3  C3  GLC01   5.240   0.984  34.354  0.70 21.57
>   C
> ATOM  4  O3  GLC01   5.144  -0.245  33.608  0.70 14.59
>   O
> ATOM  5  C4  GLC01   3.902   1.571  34.776  0.70 20.91
>   C
> ATOM  6  O4  GLC01   3.006   1.662  33.670  0.70 19.67
>   O
> ATOM  7  C5  GLC01   4.174   2.944  35.391  0.70 22.32
>   C
> ATOM  8  C6  GLC01   2.914   3.605  35.899  0.70 21.51
>   C
> ATOM  9  O6  GLC01   2.201   2.690  36.737  0.70 20.09
>   O
> ATOM 10  O5  GLC01   5.080   2.890  36.510  0.70 24.12
>   O
> ATOM 11  C1  GLC01   5.742   1.651  36.843  0.70 26.75
>   C
> ATOM 12  O1  GLC 1   5.207   0.892  37.971  0.70 30.32
>   O
> ATOM 13  C4  GLC 2   4.222   1.340  38.917  0.70 32.87
>   C
> ATOM 14  C5  GLC 2   4.753   1.239  40.352  0.70 33.51
>   C
> ATOM 15  O5  GLC 2   3.711   1.506  41.306  0.70 35.29
>   O
> ATOM 16  C6  GLC 2   5.888   2.194  40.665  0.70 34.02
>   C
> ATOM 17  O6  GLC 2   5.803   2.537  42.057  0.70 32.97
>   O
> ATOM 18  C3  GLC 2   3.072   0.331  38.851  0.70 33.72
>   C
> ATOM 19  O3  GLC 2   2.435   0.360  37.564  0.70 34.01
>   O
> ATOM 20  C2  GLC 2   2.027   0.450  39.972  0.70 35.29
>   C
> ATOM 21  O2  GLC 2   1.149  -0.684  39.932  0.70 36.32
>   O
> ATOM 22  C1  GLC 2   2.684   0.512  41.351  0.70 36.04
>   C
> ATOM 23  O1  GLC 2   1.704   0.843  42.349  0.70 36.96
>   O
> ATOM 24  C4  GLC 3   2.032   0.454  43.689  0.70 38.12
>   C
> ATOM 25  C5  GLC 3   0.810  -0.195  44.344  0.70 38.87
>   C
> ATOM 26  O5  GLC 3   1.085  -0.507  45.715  0.70 39.40
>   O
> ATOM 27  C6  GLC 3   0.372  -1.455  43.605  0.70 38.87
>   C
> ATOM 28  O6  GLC 3  -0.996  -1.300  43.220  0.70 39.09
>   O
> ATOM 29  C3  GLC 3   2.455   1.683  44.498  0.70 38.55
>   C
> ATOM 30  O3  GLC 3   3.729   2.152  44.043  0.70 38.93
>   O
> ATOM 31  C2  GLC 3   2.550   1.405  45.997  0.70 39.25
>   C
> ATOM 32  O2  GLC 3   2.700   2.646  46.700  0.70 38.44
>   O
> ATOM 33  C1  GLC 3   1.319   0.663  46.514  0.70 39.97
>   C
> ATOM 34  O1  GLC 3   1.522   0.333  47.897  0.70 41.30
>   O
> ATOM 35  C4  GLC 4   0.320  -0.039  48.583  0.70 42.19
>   C
> ATOM 36  C5  GLC 4  -0.067   0.972  49.664  0.70 42.80
>   C
> ATOM 37  O5  GLC 4  -1.358   0.617  50.163  0.70 43.08
>   O
> ATOM 38  C6  GLC 4  -0.082   2.420  49.189  0.70 43.23
>   C
> ATOM 39  O6  GLC 4  -0.900   2.532  48.019  0.70 43.36
>   O
> ATOM 40  C3  GLC 4   0.485  -1.387  49.281  0.70 42.24
>   C
> ATOM 41  O3  GLC 4   0.818  -2.397  48.323  0.70 41.16
>   O
> ATOM 42  C2  GLC 4  -0.782  -1.783  50.046  0.70 42.64
>   C
> ATOM 43  O2  GLC 4  -0.470  -2.862  50.935  0.70 42.32
>   O
> ATOM 44  C1  GLC 4  -1.375  -0.633  50.870  0.70 43.60
>   C
> ATOM 45  O1  GLCN4  -2.732  -0.947  51.190  0.70 45.14
>   O
> ATOM 46  C4  GLCN5  -3.137  -0.484  52.482  0.70 46.29
>   C
> ATOM 47  C3  GLCN5  -4.035   0.750  52.337  0.70 46.70
>   C
> ATOM 48  O3  GLCN5  -3.269   1.864  51.865  0.70 46.85
>   O
> ATOM 49  C2  GLCN5  -4.706   1.124  53.659  0.70 47.10
>   C
> ATOM 50  O2  GLCN5  -5.680   2.147  53.435  0.70 47.17
>   O
> ATOM 51  C1  GLCN5  -5.377  -0.097  54.282  0.70 47.34
>   C
> ATOM 52  O1  GLCN5  -5.958   0.264  55.539  0.70 47.48
>   O
> ATOM 53  O5  GLCN5  -4.397  -1.126  54.467  0.70 47.17
>   O
> ATOM 54  C5  GLCN5  -3.867  -1.611  53.225  0.70 46.80
>   C
> ATOM 55  C6  GLCN

Re: [gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

On 1/19/16 10:26 AM, Dries Van Rompaey wrote:

Dear gmx-users,

I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
-f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
fine. I get the same error with the -ignh flag.

WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 129 named LEU of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
discover any discrepancies. I also checked the angles in the topology, but
it looks like everything that should be applied, based on the contents of
the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.

  The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
root cause of this warning is located somewhere in the
aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
residues.

Can anyone replicate these warnings or does anyone know where they come
from?



What did you choose for the termini?  From the warnings, it looks like you chose 
"None," which is not appropriate.  The .tdb files should be overriding standard 
residue atom naming in the case of properly chosen termini.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Marco Franzoi]

You can try to add the -ter flag to pdb2gmx and manually select the n and c
ter.

Best,
Marco

Marco FRANZOI
PhD Student
University of Padua
Department of biology, V floor South
Tel: 3405086908
Mail: marco.franzo...@gmail.com

On Tue, Jan 19, 2016 at 4:26 PM, Dries Van Rompaey <
dries.vanromp...@gmail.com> wrote:

> Dear gmx-users,
>
> I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
> -f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
> fine. I get the same error with the -ignh flag.
>
> WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> WARNING: WARNING: Residue 129 named LEU of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
> aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
> discover any discrepancies. I also checked the angles in the topology, but
> it looks like everything that should be applied, based on the contents of
> the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.
>
>  The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
> root cause of this warning is located somewhere in the
> aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
> residues.
>
> Can anyone replicate these warnings or does anyone know where they come
> from?
>
> Thanks in advance,
>
> Dries
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

Hi Justin and Marco,

Thanks for your reply. I get this behaviour when I specify the default NH3+
and COO- termini through -ter, as well as when I don't use the -ter flag.
Selecting the COOH terminus type removed the warning for the C-terminus,
but selecting the NH2 terminus type did't remove the warning for the
N-terminus. That's not a very physiological state, however.

Can anyone replicate this error?

Kind regards

Dries
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

On 1/20/16 3:48 AM, Dries Van Rompaey wrote:

Hi Justin and Marco,

Thanks for your reply. I get this behaviour when I specify the default NH3+
and COO- termini through -ter, as well as when I don't use the -ter flag.
Selecting the COOH terminus type removed the warning for the C-terminus,
but selecting the NH2 terminus type did't remove the warning for the
N-terminus. That's not a very physiological state, however.

Can anyone replicate this error?



I can't trigger the same with 5.1 or with current git master.  Try from a fresh 
install and make sure no one has messed with your force field files.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

Can you remind me of the context here?  You've provided output files that 
indicate everything is fine.  If there's a problem with *input* please provide 
those files, the exact command and selections, etc.


I recall there was some terminus issue, but I've replied to a few hundred posts 
since then...


-Justin

On 2/19/16 3:50 AM, Dries Van Rompaey wrote:

Hi Justin,

Sorry for the late reply. Haven't had a chance to look at this yet. Could
you post your output files or compare the contents of yours to mine? I
chose Gromos 54a7 as my forcefield with the SPC water model. (command line
is gmx pdb2gmx -f 1aki.pdb).
I'd like to know if this is a cosmetic issue or if something else is going
on.

My files can be found here:
https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0

Thanks

Dries

On 1/20/16 3:48 AM, Dries Van Rompaey wrote:

* Hi Justin and Marco,

*>>* Thanks for your reply. I get this behaviour when I specify the default NH3+
*>* and COO- termini through -ter, as well as when I don't use the -ter flag.
*>* Selecting the COOH terminus type removed the warning for the C-terminus,
*>* but selecting the NH2 terminus type did't remove the warning for the
*>* N-terminus. That's not a very physiological state, however.
*>>* Can anyone replicate this error?
*>
I can't trigger the same with 5.1 or with current git master.  Try from a fresh
install and make sure no one has messed with your force field files.

-Justin

--



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

Sure. I pasted my original mail at the bottom.
I also followed your suggestion of trying the gromacs-master ff files, with
identical results. What I'm trying to find out is why the warning is being
triggered and if it's affecting the output in any way. My input is the 1AKI
pdb file as downloaded from the pdb. I'm converting it to .gro with the
command gmx pdb2gmx -f 1AKI.pdb, selecting the gromos54a7 force field with
spc waters.

Dear gmx-users,

I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
-f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
fine. I get the same error with the -ignh flag.

WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 129 named LEU of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
discover any discrepancies. I also checked the angles in the topology, but
it looks like everything that should be applied, based on the contents of
the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.

 The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
root cause of this warning is located somewhere in the
aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
residues.

Can anyone replicate these warnings or does anyone know where they come
from?

Thanks in advance,

Dries



On 19 February 2016 at 14:06, Justin Lemkul  wrote:

>
> Can you remind me of the context here?  You've provided output files that
> indicate everything is fine.  If there's a problem with *input* please
> provide those files, the exact command and selections, etc.
>
> I recall there was some terminus issue, but I've replied to a few hundred
> posts since then...
>
> -Justin
>
> On 2/19/16 3:50 AM, Dries Van Rompaey wrote:
>
>> Hi Justin,
>>
>> Sorry for the late reply. Haven't had a chance to look at this yet. Could
>> you post your output files or compare the contents of yours to mine? I
>> chose Gromos 54a7 as my forcefield with the SPC water model. (command line
>> is gmx pdb2gmx -f 1aki.pdb).
>> I'd like to know if this is a cosmetic issue or if something else is going
>> on.
>>
>> My files can be found here:
>> https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0
>>
>> Thanks
>>
>> Dries
>>
>> On 1/20/16 3:48 AM, Dries Van Rompaey wrote:
>>
>>> * Hi Justin and Marco,
>>>
>> *>>* Thanks for your reply. I get this behaviour when I specify the
>> default NH3+
>> *>* and COO- termini through -ter, as well as when I don't use the -ter
>> flag.
>> *>* Selecting the COOH terminus type removed the warning for the
>> C-terminus,
>> *>* but selecting the NH2 terminus type did't remove the warning for the
>> *>* N-terminus. That's not a very physiological state, however.
>> *>>* Can anyone replicate this error?
>> *>
>> I can't trigger the same with 5.1 or with current git master.  Try from a
>> fresh
>> install and make sure no one has messed with your force field files.
>>
>> -Justin
>>
>> --
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

It's because the GROMOS force fields are the only ones that explicitly list 
[angles] in the .rtp file.  All other force fields let these be generated 
automatically by the bonded structure; this is due to some subtle ways in which 
the force field files differ in their organization (use of #define for bonded 
parameters in GROMOS, etc).


So atoms get deleted when merging the .tdb hackblocks with the .rtp bondeds, 
triggering a warning that something has been deleted.  It causes no problem. 
Probably something subtle has changed, because I have never seen such warnings 
with GROMOS until recently, but these do not indicate any problem.  The bonded 
parameters change due to the altered atom types when creating termini, so the 
correct parameters should always be written.


-Justin

On 2/19/16 8:14 AM, Dries Van Rompaey wrote:

Sure. I pasted my original mail at the bottom.
I also followed your suggestion of trying the gromacs-master ff files, with
identical results. What I'm trying to find out is why the warning is being
triggered and if it's affecting the output in any way. My input is the 1AKI
pdb file as downloaded from the pdb. I'm converting it to .gro with the
command gmx pdb2gmx -f 1AKI.pdb, selecting the gromos54a7 force field with
spc waters.

Dear gmx-users,

I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
-f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
fine. I get the same error with the -ignh flag.

WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 129 named LEU of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
discover any discrepancies. I also checked the angles in the topology, but
it looks like everything that should be applied, based on the contents of
the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.

  The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
root cause of this warning is located somewhere in the
aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
residues.

Can anyone replicate these warnings or does anyone know where they come
from?

Thanks in advance,

Dries



On 19 February 2016 at 14:06, Justin Lemkul  wrote:



Can you remind me of the context here?  You've provided output files that
indicate everything is fine.  If there's a problem with *input* please
provide those files, the exact command and selections, etc.

I recall there was some terminus issue, but I've replied to a few hundred
posts since then...

-Justin

On 2/19/16 3:50 AM, Dries Van Rompaey wrote:


Hi Justin,

Sorry for the late reply. Haven't had a chance to look at this yet. Could
you post your output files or compare the contents of yours to mine? I
chose Gromos 54a7 as my forcefield with the SPC water model. (command line
is gmx pdb2gmx -f 1aki.pdb).
I'd like to know if this is a cosmetic issue or if something else is going
on.

My files can be found here:
https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0

Thanks

Dries

On 1/20/16 3:48 AM, Dries Van Rompaey wrote:


* Hi Justin and Marco,


*>>* Thanks for your reply. I get this behaviour when I specify the
default NH3+
*>* and COO- termini through -ter, as well as when I don't use the -ter
flag.
*>* Selecting the COOH terminus type removed the warning for the
C-terminus,
*>* but selecting the NH2 terminus type did't remove the warning for the
*>* N-terminus. That's not a very physiological state, however.
*>>* Can anyone replicate this error?
*>
I can't trigger the same with 5.1 or with current git master.  Try from a
fresh
install and make sure no one has messed with your force field files.

-Justin

--



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users

Re: [gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

That's good to know. Thanks for the clarifications.

On 19 February 2016 at 14:22, Justin Lemkul  wrote:

>
> It's because the GROMOS force fields are the only ones that explicitly
> list [angles] in the .rtp file.  All other force fields let these be
> generated automatically by the bonded structure; this is due to some subtle
> ways in which the force field files differ in their organization (use of
> #define for bonded parameters in GROMOS, etc).
>
> So atoms get deleted when merging the .tdb hackblocks with the .rtp
> bondeds, triggering a warning that something has been deleted.  It causes
> no problem. Probably something subtle has changed, because I have never
> seen such warnings with GROMOS until recently, but these do not indicate
> any problem.  The bonded parameters change due to the altered atom types
> when creating termini, so the correct parameters should always be written.
>
> -Justin
>
>
> On 2/19/16 8:14 AM, Dries Van Rompaey wrote:
>
>> Sure. I pasted my original mail at the bottom.
>> I also followed your suggestion of trying the gromacs-master ff files,
>> with
>> identical results. What I'm trying to find out is why the warning is being
>> triggered and if it's affecting the output in any way. My input is the
>> 1AKI
>> pdb file as downloaded from the pdb. I'm converting it to .gro with the
>> command gmx pdb2gmx -f 1AKI.pdb, selecting the gromos54a7 force field with
>> spc waters.
>>
>> Dear gmx-users,
>>
>> I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
>> -f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
>> fine. I get the same error with the -ignh flag.
>>
>> WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
>> mapped
>> to an entry in the topology database, but the atom H used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>>
>> WARNING: WARNING: Residue 129 named LEU of a molecule in the input file
>> was
>> mapped
>> to an entry in the topology database, but the atom O used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>>
>> I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
>> aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
>> discover any discrepancies. I also checked the angles in the topology, but
>> it looks like everything that should be applied, based on the contents of
>> the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.
>>
>>   The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
>> root cause of this warning is located somewhere in the
>> aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
>> residues.
>>
>> Can anyone replicate these warnings or does anyone know where they come
>> from?
>>
>> Thanks in advance,
>>
>> Dries
>>
>>
>>
>> On 19 February 2016 at 14:06, Justin Lemkul  wrote:
>>
>>
>>> Can you remind me of the context here?  You've provided output files that
>>> indicate everything is fine.  If there's a problem with *input* please
>>> provide those files, the exact command and selections, etc.
>>>
>>> I recall there was some terminus issue, but I've replied to a few hundred
>>> posts since then...
>>>
>>> -Justin
>>>
>>> On 2/19/16 3:50 AM, Dries Van Rompaey wrote:
>>>
>>> Hi Justin,

 Sorry for the late reply. Haven't had a chance to look at this yet.
 Could
 you post your output files or compare the contents of yours to mine? I
 chose Gromos 54a7 as my forcefield with the SPC water model. (command
 line
 is gmx pdb2gmx -f 1aki.pdb).
 I'd like to know if this is a cosmetic issue or if something else is
 going
 on.

 My files can be found here:

 https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0

 Thanks

 Dries

 On 1/20/16 3:48 AM, Dries Van Rompaey wrote:

 * Hi Justin and Marco,
>
> *>>* Thanks for your reply. I get this behaviour when I specify the
 default NH3+
 *>* and COO- termini through -ter, as well as when I don't use the -ter
 flag.
 *>* Selecting the COOH terminus type removed the warning for the
 C-terminus,
 *>* but selecting the NH2 terminus type did't remove the warning for the
 *>* N-terminus. That's not a very physiological state, however.
 *>>* Can anyone replicate this error?
 *>
 I can't trigger the same with 5.1 or with current git master.  Try from
 a
 fresh
 install and make sure no one has messed with your force field files.

 -Justin

 --


 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II

Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/30/16 10:41 PM, Brett wrote:

Dear All,

When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with force
field, it gave me the warning as following,

"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
"
I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
exactly my C-terminal residue.

Here I copied the coordinates part for the N- and C-terminal residues here:

ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   N
ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   C
ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   C
ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   C
ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   O
ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   O
ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   C
ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   O
ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   N
(Residue 1 named ASP by GROMACS)
.

ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   O
ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   N
ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   C
ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   C
ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   C
ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   C
ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   C
ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   C
ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   O
ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   O
(Residue 42 named ILE  by GROMACS)
TER
END

I myself cannot find anything wrong for my 2 terminal residues.

Will you please take a look to see how to modify the 2 terminal residues so that
the pdb2gmx will not give the warning messages?

I am looking forward to getting a reply from you.



The only way the above errors would show up is if you chose "None" for your 
termini; choosing an appropriate NH3+/COO- will correct this. Note you have two 
"O" in your C-terminal ILE, which is wrong as there should only be one, the 
other should be OXT or whatever the force field wants (but again, the .tdb 
patching mechanism takes care of this).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx & terminal residues

[Brett]

Dear Justin and All,

For terminal residue, regardless I select 0, 1, 2, the error messages always 
exist.

I have opened the pdb by swiss deep view and resaved it, the same error message 
still exist.


However if I choose force field 6: AMBER99SB-ILDN protein, the error message 
disappear.

Will you please give suggestions on getting rid of the warning messages for the 
terminal residues by pdb2gmx?

Brett









At 2016-03-31 19:12:38, "Justin Lemkul"  wrote:
>
>
>On 3/30/16 10:41 PM, Brett wrote:
>> Dear All,
>>
>> When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with 
>> force
>> field, it gave me the warning as following,
>>
>> "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom H used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>>
>>
>>
>> WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom O used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>> "
>> I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
>> exactly my C-terminal residue.
>>
>> Here I copied the coordinates part for the N- and C-terminal residues here:
>>
>> ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   
>> N
>> ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   
>> C
>> ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   
>> C
>> ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   
>> C
>> ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   
>> O
>> ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   
>> O
>> ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   
>> C
>> ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   
>> O
>> ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   
>> N
>> (Residue 1 named ASP by GROMACS)
>> .
>>
>> ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   
>> O
>> ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   
>> N
>> ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   
>> C
>> ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   
>> C
>> ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   
>> C
>> ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   
>> C
>> ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   
>> C
>> ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   
>> C
>> ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   
>> O
>> ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   
>> O
>> (Residue 42 named ILE  by GROMACS)
>> TER
>> END
>>
>> I myself cannot find anything wrong for my 2 terminal residues.
>>
>> Will you please take a look to see how to modify the 2 terminal residues so 
>> that
>> the pdb2gmx will not give the warning messages?
>>
>> I am looking forward to getting a reply from you.
>>
>
>The only way the above errors would show up is if you chose "None" for your 
>termini; choosing an appropriate NH3+/COO- will correct this. Note you have 
>two 
>"O" in your C-terminal ILE, which is wrong as there should only be one, the 
>other should be OXT or whatever the force field wants (but again, the .tdb 
>patching mechanism takes care of this).
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-

Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/31/16 8:18 AM, Brett wrote:

Dear Justin and All,

For terminal residue, regardless I select 0, 1, 2, the error messages always 
exist.

I have opened the pdb by swiss deep view and resaved it, the same error message 
still exist.


However if I choose force field 6: AMBER99SB-ILDN protein, the error message 
disappear.

Will you please give suggestions on getting rid of the warning messages for the 
terminal residues by pdb2gmx?



Please provide the full, unfiltered screen output from a functional and 
nonfunctional run through pdb2gmx.  There is no reason this shouldn't work out 
of the box.


-Justin


Brett









At 2016-03-31 19:12:38, "Justin Lemkul"  wrote:



On 3/30/16 10:41 PM, Brett wrote:

Dear All,

When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with force
field, it gave me the warning as following,

"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
"
I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
exactly my C-terminal residue.

Here I copied the coordinates part for the N- and C-terminal residues here:

ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   N
ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   C
ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   C
ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   C
ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   O
ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   O
ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   C
ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   O
ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   N
(Residue 1 named ASP by GROMACS)
.

ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   O
ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   N
ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   C
ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   C
ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   C
ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   C
ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   C
ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   C
ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   O
ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   O
(Residue 42 named ILE  by GROMACS)
TER
END

I myself cannot find anything wrong for my 2 terminal residues.

Will you please take a look to see how to modify the 2 terminal residues so that
the pdb2gmx will not give the warning messages?

I am looking forward to getting a reply from you.



The only way the above errors would show up is if you chose "None" for your
termini; choosing an appropriate NH3+/COO- will correct this. Note you have two
"O" in your C-terminal ILE, which is wrong as there should only be one, the
other should be OXT or whatever the force field wants (but again, the .tdb
patching mechanism takes care of this).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

=

Re: [gmx-users] pdb2gmx & terminal residues

[Brett]

Dear Justin and All,

The full screen output was as following and I am looking forward to getting a 
reply from you.




 gmx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh
  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar  
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner 
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk  
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf  
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh


Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
14

Using the Gromos54a7 force field in directory gromos54a7.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/watermodels.dat

Select the Water Model:
 1: SPCsimple point charge, recommended
 2: SPC/E  extended simple point charge
 3: None
1
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading practice.pdb...
Read 331 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 42 residues with 331 atoms

  chain  #res #atoms
  1 'N'42331 

All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database... (gromos54a7)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 108
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 'N' (331 atoms, 42 residues)
Identified residue ASP288 as a starting terminus.
Identified residue ILE329 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ASP-288: NH3+
End terminus ILE-329: COO-
Checking for duplicate atoms
Now there are 330 atoms. Deleted 1 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 42 residues with 417 atoms
Making bonds...
Number of bonds was 424, now 419
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of t

Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/31/16 10:41 AM, Brett wrote:

Dear Justin and All,

The full screen output was as following and I am looking forward to getting a 
reply from you.




  gmx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh
   :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
   gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh


Select the Force Field:
 From '/usr/local/gromacs/share/gromacs/top':
  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
  4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
  5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
  6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
  7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
14

Using the Gromos54a7 force field in directory gromos54a7.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/watermodels.dat

Select the Water Model:
  1: SPCsimple point charge, recommended
  2: SPC/E  extended simple point charge
  3: None
1
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading practice.pdb...
Read 331 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 42 residues with 331 atoms

   chain  #res #atoms
   1 'N'42331

All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database... (gromos54a7)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 108
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 'N' (331 atoms, 42 residues)
Identified residue ASP288 as a starting terminus.
Identified residue ILE329 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ASP-288: NH3+
End terminus ILE-329: COO-
Checking for duplicate atoms
Now there are 330 atoms. Deleted 1 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 42 residues with 417 atoms
Making bonds...
Number of bonds was 424, now 419
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topo

Re: [gmx-users] pdb2gmx question - protonation

[Justin Lemkul]

On 2/6/15 9:29 PM, Agnivo Gosai wrote:

Dear Users

I am using the default settings for the pdb2gmx program and I leave the
protonation of AA residues to the program.

Can anybody tell me about the default protonation states of LYS, ASP, GLU,
CYS or HIS employed by pdb2gmx ?

I checked the manual but it is not explicitly mentioned. Is there any
literature available. I am sorry if I am asking for too much.



It is explained by reading pdb2gmx -h.  The default protonation states for all 
titratable residues are listed.  Histidine protonation is determined by 
proximity of groups that can participate in hydrogen bonding.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx fatal error

[Justin Lemkul]

On 11/7/18 1:05 PM, Ali Khodayari wrote:

Dear gmx users,

  


I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names
were modified according to the rtp file of the force field. Yet, I get the
following error while I perform pdb2gmx command:

  


Fatal error:

Residue 4 named GLC of a molecule in the input file was mapped to an entry
in the topology database, but the atom C6 used in that entry is not found in
the input file. Perhaps your atom and/or residue naming needs to be fixed."

  


I also tried to delete the hydrogens in the pdb file but the error changed
to the following:

  


Fatal error:

Residue 876814369 named GLC of a molecule in the input file was mapped to an
entry in the topology database, but the atom C3 used in an interaction of
type improper in that entry is not found in the input file. Perhaps your
atom and/or residue naming needs to be fixed.

  


Ignoring the hydrogens through -ignh will give the first error as well.
Then I added the GLC residue to the residuetypes.dat and the error changed
to:


Your problem is not related to hydrogens. pdb2gmx is complaining about 
carbon nomenclature.


http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

  


Fatal error:

atom N not found in buiding block 1GLC while combining tdb and rtp

  


This error comes from letting pdb2gmx apply default protein terminal 
patches. For a carbohydrate, you probably should have definitions for 
properly constructed reducing and non-reducing ends (e.g. different from 
internal residues) and apply no terminal patching.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx fatal error

[Ali Khodayari]

Dear Justin,

Thank you for your response. Yet, I have not been able to solve the problem.

The structure looks fine but gromacs is complaining about a dangling atom at
one of the terminal ends, if I choose no terminal to be added. While,
assigning a terminal to the ends (which I don't understand why), results to
another error, which to me seems bizarre. It is still complaining about an
atom (C6) which is not found in the input file (.rtp?), however, it is
indeed one of the atoms in the rtp file. 
Here is what it looks like in the rtp file:

[ GLC0 ]
 [ atoms ]
   C4   CH1R0.23200 1   
   O4   OA -0.64200 1
   HO4  H   0.41000 1
   C3   CH1R0.23200 2
   O3OA-0.64200 2
  HO3 H 0.41000 2
   C2   CH1R0.23200 3
   O2OA-0.64200 3
  HO2 H 0.41000 3
   C6   CH2 0.23200 4
   O6OA-0.64200 4
  HO6 H 0.41000 4
   C5   CH1R0.23200 0
   O5OR-0.46400 0
   C1   CH1R0.46400 0
   O1OE-0.46400 0

And the pdb input file is:

ATOM  1  C1  GLC01  3.992   3.199   3.177  1.00  0.04
C
ATOM  2  C2  GLC01  3.597   2.204   2.072  1.00  0.04
C
ATOM  3  C3  GLC01  4.231   2.633   0.737  1.00  0.04
C
ATOM  4  C4  GLC01  3.713   4.036   0.378  1.00  0.04
C
ATOM  5  C5  GLC01  4.096   5.017   1.502  1.00  0.04
C
ATOM  6  C6  GLC01  3.581   6.419   1.132  1.00  0.04
C
ATOM  7  O2  GLC01  4.094   0.828   2.442  1.00  0.04
O
ATOM  8  O5  GLC01  3.476   4.569   2.805  1.00  0.04
O
ATOM  9  O6  GLC01  4.207   6.834  -0.178  1.00  0.04
O
ATOM 10  H1  GLC01  5.128   3.219   3.268  1.00  0.00
H
ATOM 11  H2  GLC01  2.462   2.181   1.967  1.00  0.00
H
ATOM 12  H3  GLC01  5.366   2.661   0.847  1.00  0.00
H
ATOM 13  H4  GLC01  2.578   4.005   0.271  1.00  0.00
H
ATOM 14  H5  GLC01  5.230   5.045   1.611  1.00  0.00
H
ATOM 15  H61 GLC01  3.858   7.165   1.950  1.00  0.00
H
ATOM 16  H62 GLC01  2.449   6.385   1.015  1.00  0.00
H
ATOM 17  HO2 GLC01  5.198   0.853   2.551  1.00  0.00
H
ATOM 18  HO6 GLC01  5.313   6.850  -0.083  1.00  0.00
H
ATOM 19  O4  GLC02  4.312   4.595   9.824  1.00  0.04
O
ATOM 20  C1  GLC02  3.708   4.145   8.515  1.00  0.04
C
ATOM 21  C2  GLC02  4.109   5.126   7.399  1.00  0.04
C
ATOM 22  C3  GLC02  3.497   4.668   6.062  1.00  0.04
C
ATOM 23  C4  GLC02  4.005   3.250   5.730  1.00  0.04
C
ATOM 24  C5  GLC02  3.616   2.295   6.877  1.00  0.04
C
ATOM 25  C6  GLC02  4.151   0.877   6.596  1.00  0.04
C
ATOM 26  O2  GLC02  3.601   6.506   7.743  1.00  0.04
O
ATOM 27  O3  GLC02  3.909   5.661   5.002  1.00  0.04
O
ATOM 28  HO4 GLC02  4.850   3.729  10.263  1.00  0.00
H
ATOM 29  O1  GLC01  3.396   2.685   4.467  1.00  0.04
O
ATOM 30  O5  GLC02  4.225   2.770   8.173  1.00  0.04
O
ATOM 31  O6  GLC02  3.558   0.309   5.328  1.00  0.04
O
ATOM 32  H1  GLC02  2.572   4.115   8.609  1.00  0.00
H
ATOM 33  H2  GLC02  5.244   5.151   7.307  1.00  0.00
H
ATOM 34  H3  GLC02  2.361   4.651   6.153  1.00  0.00
H
ATOM 35  H4  GLC02  5.141   3.258   5.636  1.00  0.00
H
ATOM 36  H5  GLC02  2.480   2.262   6.979  1.00  0.00
H
ATOM 37  H61 GLC02  3.879   0.196   7.468  1.00  0.00
H
ATOM 38  H62 GLC02  5.286   0.920   6.494  1.00  0.00
H
ATOM 39  HO2 GLC02  2.496   6.480   7.836  1.00  0.00
H
ATOM 40  HO3 GLC02  5.015   5.674   4.919  1.00  0.00
H
ATOM 41  HO6 GLC02  2.453   0.270   5.418  1.00  0.00
H
ATOM 42  O3  GLC01  3.852   1.653  -0.348  1.00  0.00
O
ATOM 43  HO3 GLC01  4.305   1.969  -1.311  1.00  0.00
H
END

The error is given as a result of the command:  gmx pdb2gmx -f
cellobiose.pdb -o cellobiose.gro -ignh -ter

The error:
Fatal error:
Residue 4 named GLC0 of a molecule in the input file was mapped
to an entry in the topology database, but the atom C6 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

Do you have any idea why it is happening?
Thank you in advanced.
Regards,
Ali





-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Justin
Lemkul
Sent: donderdag 8 november 2018 13:57
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb2gmx fatal error



On 11/7/18 1:05 PM, Ali Khodayari wrote:
> Dear gmx users,
>
>   
>
> I am trying to simulate a cellobiose, using GROMOS53a6CARB

Re: [gmx-users] pdb2gmx fatal error

[Justin Lemkul]

On 11/8/18 1:37 PM, Ali Khodayari wrote:

Dear Justin,

Thank you for your response. Yet, I have not been able to solve the problem.

The structure looks fine but gromacs is complaining about a dangling atom at
one of the terminal ends, if I choose no terminal to be added. While,


You can't "see" a dangling bond by visualizing the structure. That term 
refers exclusively to an incomplete terminus in terms of the *topology* 
that is being generated for the system. Maybe atoms are missing or an 
inappropriate terminal patch is being applied; either would generate 
that error. But again I emphasize the fact that a chain of glucose has 
first and last residues that are structurally and topologically 
different from internal, linked monomers. It's basic chemistry.





ATOM 27  O3  GLC02  3.909   5.661   5.002  1.00  0.04
O
ATOM 28  HO4 GLC02  4.850   3.729  10.263  1.00  0.00
H
ATOM 29  O1  GLC01  3.396   2.685   4.467  1.00  0.04
O


Here's your problem - your residue numbers alternate back and forth 
between 1 and 2. pdb2gmx ignores these and uses its own numbering, 
incrementing the internal counter whenever the residue number changes. 
So to pdb2gmx, your input file is full of incomplete residues.



ATOM 30  O5  GLC02  4.225   2.770   8.173  1.00  0.04
O
ATOM 31  O6  GLC02  3.558   0.309   5.328  1.00  0.04
O
ATOM 32  H1  GLC02  2.572   4.115   8.609  1.00  0.00
H
ATOM 33  H2  GLC02  5.244   5.151   7.307  1.00  0.00
H
ATOM 34  H3  GLC02  2.361   4.651   6.153  1.00  0.00
H
ATOM 35  H4  GLC02  5.141   3.258   5.636  1.00  0.00
H
ATOM 36  H5  GLC02  2.480   2.262   6.979  1.00  0.00
H
ATOM 37  H61 GLC02  3.879   0.196   7.468  1.00  0.00
H
ATOM 38  H62 GLC02  5.286   0.920   6.494  1.00  0.00
H
ATOM 39  HO2 GLC02  2.496   6.480   7.836  1.00  0.00
H
ATOM 40  HO3 GLC02  5.015   5.674   4.919  1.00  0.00
H
ATOM 41  HO6 GLC02  2.453   0.270   5.418  1.00  0.00
H
ATOM 42  O3  GLC01  3.852   1.653  -0.348  1.00  0.00
O


As above, now you're again going back and forth between 1 and 2, so 
pdb2gmx sees a new residue, which is not correct.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx fatal error

[Ali Khodayari]

Dear Justin,

Thank you for your full explanation. That made it all clear now.

Kind regards,
Ali

> On 13 Nov 2018, at 00:57, Justin Lemkul  wrote:
> 
> 
> 
> On 11/8/18 1:37 PM, Ali Khodayari wrote:
>> Dear Justin,
>> 
>> Thank you for your response. Yet, I have not been able to solve the problem.
>> 
>> The structure looks fine but gromacs is complaining about a dangling atom at
>> one of the terminal ends, if I choose no terminal to be added. While,
> 
> You can't "see" a dangling bond by visualizing the structure. That term 
> refers exclusively to an incomplete terminus in terms of the *topology* that 
> is being generated for the system. Maybe atoms are missing or an 
> inappropriate terminal patch is being applied; either would generate that 
> error. But again I emphasize the fact that a chain of glucose has first and 
> last residues that are structurally and topologically different from 
> internal, linked monomers. It's basic chemistry.
> 
> 
> 
>> ATOM 27  O3  GLC02  3.909   5.661   5.002  1.00  0.04
>> O
>> ATOM 28  HO4 GLC02  4.850   3.729  10.263  1.00  0.00
>> H
>> ATOM 29  O1  GLC01  3.396   2.685   4.467  1.00  0.04
>> O
> 
> Here's your problem - your residue numbers alternate back and forth between 1 
> and 2. pdb2gmx ignores these and uses its own numbering, incrementing the 
> internal counter whenever the residue number changes. So to pdb2gmx, your 
> input file is full of incomplete residues.
> 
>> ATOM 30  O5  GLC02  4.225   2.770   8.173  1.00  0.04
>> O
>> ATOM 31  O6  GLC02  3.558   0.309   5.328  1.00  0.04
>> O
>> ATOM 32  H1  GLC02  2.572   4.115   8.609  1.00  0.00
>> H
>> ATOM 33  H2  GLC02  5.244   5.151   7.307  1.00  0.00
>> H
>> ATOM 34  H3  GLC02  2.361   4.651   6.153  1.00  0.00
>> H
>> ATOM 35  H4  GLC02  5.141   3.258   5.636  1.00  0.00
>> H
>> ATOM 36  H5  GLC02  2.480   2.262   6.979  1.00  0.00
>> H
>> ATOM 37  H61 GLC02  3.879   0.196   7.468  1.00  0.00
>> H
>> ATOM 38  H62 GLC02  5.286   0.920   6.494  1.00  0.00
>> H
>> ATOM 39  HO2 GLC02  2.496   6.480   7.836  1.00  0.00
>> H
>> ATOM 40  HO3 GLC02  5.015   5.674   4.919  1.00  0.00
>> H
>> ATOM 41  HO6 GLC02  2.453   0.270   5.418  1.00  0.00
>> H
>> ATOM 42  O3  GLC01  3.852   1.653  -0.348  1.00  0.00
>> O
> 
> As above, now you're again going back and forth between 1 and 2, so pdb2gmx 
> sees a new residue, which is not correct.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
> ==
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx , or equivalent

[Justin Lemkul]

On 11/15/19 12:48 PM, Ling Chan wrote:

Hello Colleagues,

I would like to run Gromacs on some proteins that I have prepared. I see that 
you can obtain Gromacs input files using pdb2gmx. Just wonder if one can 
prevent pdb2gmx from tempering with your protein? I mean, pdb2gmx does a bunch 
of clean ups. I would like it to skip the clean up stage.

I see that one can either let the clean up happen automatically, or have you 
tell it interactively whenever there is a decision to make. I would just like 
it to respect my structure – in the sense that no hydrogen is added or removed.


If you provide pdb2gmx with a structure that conforms to the force 
field's expectations of atom and residue naming, then pdb2gmx won't 
change anything about it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx , or equivalent

[Justin Lemkul]

On 11/15/19 5:15 PM, Ling Chan wrote:

I see, thank you Justin. Suppose you mean ASP vs ASH, HID, HIE, HIP, etc.?


Yes, as well as all the constituent hydrogen atoms.


But how about disulfide bridges? Does pdb2gmx respect SSBOND and / or CONECT 
records in the PDB? Perhaps it will re-evaluate them regardless?


pdb2gmx automatically detects them based on S-S distances. If you want 
to override/change what pdb2gmx detects, you have to do that 
interactively. CONECT records are never used.



Also, I see on the pdb2gmx manual page that the default glutamine is charged. 
What does it mean?


Glutamine is almost never charged and most force fields don't support 
it. There is a -gln option that allows you to define protonation state, 
but if pdb2gmx sees GLN it is the neutral form.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PDB2GMX Fatal Error

[Reza Esmaeili]

Use -ignh in pdb2gmx.

> On Mar 1, 2017, at 10:22, Syed Azeem  wrote:
> 
> Hi all,
> 
> I tried passing a predicted peptide (16-mer) into GMX and ended up
> with a fatal error regarding hydrogen. I tried ignoring the hydrogens
> using -ignh command. But I'll need to calculate H-bonds for the next
> analysis, as I'll dock this peptide into a target protein.
> 
> Fatal error:
> Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 atoms
> while sorting atoms.
> 
> For a hydrogen, this can be a different protonation state, or it
> might have had a different number in the PDB file and was rebuilt
> (it might for instance have been H3, and we only expected H1 & H2).
> Note that hydrogens might have been added to the entry for the N-terminus.
> Remove this hydrogen or choose a different protonation state to solve it.
> Option -ignh will ignore all hydrogens in the input.
> 
> How to solve this issue?
> 
> Thanks in advance
> 
> Azeem
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PDB2GMX Fatal Error

[Syed Azeem]

>
> Use -ignh in pdb2gmx.
Hi Reza,

I tried -ignh, it's working fine.

But i need to calculate H-bonds after docking the same peptide. Then
the same error will crop up and I won't be able to calculate H-bonds.

>> On Mar 1, 2017, at 10:22, Syed Azeem  wrote:
>>
>> Hi all,
>>
>> I tried passing a predicted peptide (16-mer) into GMX and ended up
>> with a fatal error regarding hydrogen. I tried ignoring the hydrogens
>> using -ignh command. But I'll need to calculate H-bonds for the next
>> analysis, as I'll dock this peptide into a target protein.
>>
>> Fatal error:
>> Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 atoms
>> while sorting atoms.
>>
>> For a hydrogen, this can be a different protonation state, or it
>> might have had a different number in the PDB file and was rebuilt
>> (it might for instance have been H3, and we only expected H1 & H2).
>> Note that hydrogens might have been added to the entry for the
>> N-terminus.
>> Remove this hydrogen or choose a different protonation state to solve it.
>> Option -ignh will ignore all hydrogens in the input.
>>
>> How to solve this issue?
>>
>> Thanks in advance
>>
>> Azeem
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PDB2GMX Fatal Error

[Justin Lemkul]

On 3/1/17 3:23 AM, Syed Azeem wrote:


Use -ignh in pdb2gmx.

Hi Reza,

I tried -ignh, it's working fine.

But i need to calculate H-bonds after docking the same peptide. Then
the same error will crop up and I won't be able to calculate H-bonds.



The use of -ignh has nothing to do with whether or not you can calculate 
hydrogen bonds.


The more complete explanation about -ignh is that H atoms in the input 
coordinates are ignored, then rebuilt according to the force field's .hdb file. 
Your problem was that your H atom nomenclature was non-standard, or at least did 
not conform to the force field's expectations, so you got a fatal error.  You 
can easily confirm in the topology and coordinates produced when using -ignh 
that in fact all of the H you need are there.  pdb2gmx just rebuilt them so you 
didn't have to waste time renaming all your non-conforming H atoms.


-Justin


On Mar 1, 2017, at 10:22, Syed Azeem  wrote:

Hi all,

I tried passing a predicted peptide (16-mer) into GMX and ended up
with a fatal error regarding hydrogen. I tried ignoring the hydrogens
using -ignh command. But I'll need to calculate H-bonds for the next
analysis, as I'll dock this peptide into a target protein.

Fatal error:
Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the
N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.

How to solve this issue?

Thanks in advance

Azeem


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] PDB2GMX Fatal Error

[Syed Azeem]

>>> Use -ignh in pdb2gmx.
>> Hi Reza,
>>
>> I tried -ignh, it's working fine.
>>
>> But i need to calculate H-bonds after docking the same peptide. Then
>> the same error will crop up and I won't be able to calculate H-bonds.
>>
>
> The use of -ignh has nothing to do with whether or not you can calculate
> hydrogen bonds.
>
> The more complete explanation about -ignh is that H atoms in the input
> coordinates are ignored, then rebuilt according to the force field's .hdb
> file.
> Your problem was that your H atom nomenclature was non-standard, or at least
> did
> not conform to the force field's expectations, so you got a fatal error.
> You
> can easily confirm in the topology and coordinates produced when using -ignh
>
> that in fact all of the H you need are there.  pdb2gmx just rebuilt them so
> you
> didn't have to waste time renaming all your non-conforming H atoms.
>
> -Justin
Now I understood the -ignh option.
Thanks for the explanation

-Azeem
 On Mar 1, 2017, at 10:22, Syed Azeem 
 wrote:

 Hi all,

 I tried passing a predicted peptide (16-mer) into GMX and ended up
 with a fatal error regarding hydrogen. I tried ignoring the hydrogens
 using -ignh command. But I'll need to calculate H-bonds for the next
 analysis, as I'll dock this peptide into a target protein.

 Fatal error:
 Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 atoms
 while sorting atoms.

 For a hydrogen, this can be a different protonation state, or it
 might have had a different number in the PDB file and was rebuilt
 (it might for instance have been H3, and we only expected H1 & H2).
 Note that hydrogens might have been added to the entry for the
 N-terminus.
 Remove this hydrogen or choose a different protonation state to solve
 it.
 Option -ignh will ignore all hydrogens in the input.

 How to solve this issue?

 Thanks in advance

 Azeem
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Justin Lemkul]

On 4/25/15 12:00 AM, Alex wrote:

Ahoy,

What I have here is a 100% precisely set up periodic ssdna chain of
six residues without termini. The goal is to get the 'polymerization'
across the box. So, I boxed the chain and set up the periodicity pretty much
perfectly.

To test, translation in the direction of periodicity by the
periodicity constant results in bonds perfectly recognized by things like VMD or
pymol (in the concatenated structure).

When running pdb2gmx on the boxed structure, the periodicity seems to
be ignored and then expectedly I get a fatal error with a custom FF that works
fine on finite chains.
x2top sees pbc, but we're not using it here. So, no topology in sight.

Any ideas?


pdb2gmx isn't designed to intuitively handle such cases.  The best way to go 
about it is:


1. Run pdb2gmx normally to add H that you might need and to apply patching such 
that you have a phosphate on one end and an alcohol on the other (presumably you 
already have this last part done and have suitable .tdb entries).


2. Delete unnecessary atoms from the termini.

3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't 
complain at you about dangling termini.


4. Manually edit the topology to introduce the needed bond, angles, and 
dihedrals.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Alex]

Yeah, I was trying to avoid that last part. You can tell by now how much I
dislike uhm doing work. :) I'll try it, thanks.

Alex


JL> 4. Manually edit the topology to introduce the needed bond, angles, and 
dihedrals.

JL> -Justin


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Alex]

Justin,

I am not entirely sure I understand your sequence of steps. Why do you
want to first run it normally, but then also without adding the
hydrogens? The hydrogens (a total of two) are only added at the
termini by default, and in the final product there's no
need for them anyway.

Here's what I'm able to understand: run as usual, delete all bonded data
relevant to termini, add bonded descriptions for the residues at the
boundary, modify pdb to remove termini (actually, I can generate the
periodic ones automatically). Am I missing something that
should make my life easier?

Also, is there a way to automate this by modifying the forcefield?
See, right now (on the periodic structure without termini) pdb2gmx
sees the first residue and looks it up as one with a terminus, which
is really the gist of the error it throws, so I doubt it even gets to
the point of looking at the boundary. Is it that the utility behavior
cannot be changed at the ff level, and thus our only
option is manual modification of the topology?

Thank you,

Alex

JL> pdb2gmx isn't designed to intuitively handle such cases.  The best way to go
JL> about it is:

JL> 1. Run pdb2gmx normally to add H that you might need and to apply patching 
such
JL> that you have a phosphate on one end and an alcohol on the other 
(presumably you
JL> already have this last part done and have suitable .tdb entries).

JL> 2. Delete unnecessary atoms from the termini.

JL> 3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't
JL> complain at you about dangling termini.

JL> 4. Manually edit the topology to introduce the needed bond, angles, and 
dihedrals.

JL> -Justin



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Justin Lemkul]

On 4/25/15 11:34 PM, Alex wrote:

Justin,

I am not entirely sure I understand your sequence of steps. Why do you
want to first run it normally, but then also without adding the
hydrogens? The hydrogens (a total of two) are only added at the
termini by default, and in the final product there's no
need for them anyway.



I was speaking in generalizations; most starting structures need H added.  If 
that's not relevant, then just skip it.



Here's what I'm able to understand: run as usual, delete all bonded data
relevant to termini, add bonded descriptions for the residues at the
boundary, modify pdb to remove termini (actually, I can generate the
periodic ones automatically). Am I missing something that
should make my life easier?



In theory, if you assign a phosphate as one of your termini (rather than the 
normal C5'-OH and C3'-OH) then you have to modify very little.



Also, is there a way to automate this by modifying the forcefield?
See, right now (on the periodic structure without termini) pdb2gmx
sees the first residue and looks it up as one with a terminus, which
is really the gist of the error it throws, so I doubt it even gets to
the point of looking at the boundary. Is it that the utility behavior
cannot be changed at the ff level, and thus our only
option is manual modification of the topology?


It's got nothing to do with the force field and everything to do with software 
and convention.  It's the same case with cyclic peptides or circular DNA.  It 
can be made to work, but that's not really how the software was designed because 
it's not a common procedure.  DNA is assumed to be a linear polymer of finite 
length.  If you don't do that, it's up to you to hack it together.


The force field parameters for a phosphodiester are the same in a linear, finite 
DNA as they will be in your infinite chain.  The problem is in telling pdb2gmx 
"don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)."


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Alex]

JL> The force field parameters for a phosphodiester are the same in a linear, 
finite
JL> DNA as they will be in your infinite chain.

I didn't mean that anything would need to be changed in the description of 
residues. The FF handles a
finite chain perfectly.

JL> The problem is in telling pdb2gmx
JL> "don't link i,i+1 here, instead link i,i+(some number of intervening 
nucleotides)."

This is exactly what I meant, the linking. Is there a way to achieve this
without messing with the code? I just haven't looked at the code, so
if you think I'm being a cheeky little bastard, I'll accept that. :)

Thanks,

Alex


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Tsjerk Wassenaar]

Hi Alex,

I think the best way is to extend the chain, such that you get an overlap
between both ends. So for a stretch of DNA

ACGT

You would generate

TACGTA

Then you strip off the terminal atoms and rewire the links over the
boundary. It requires renumbering the topology and at first looks a bit
cumbersome, but this ensures all the links are correct and the
modifications of the termini have no effect, and it's not very hard to
script. And, of course, scripting it is a one time effort to avoid doing it
manually later.

Cheers,

Tsjerk
On Apr 26, 2015 5:55 AM, "Alex"  wrote:

> JL> The force field parameters for a phosphodiester are the same in a
> linear, finite
> JL> DNA as they will be in your infinite chain.
>
> I didn't mean that anything would need to be changed in the description of
> residues. The FF handles a
> finite chain perfectly.
>
> JL> The problem is in telling pdb2gmx
> JL> "don't link i,i+1 here, instead link i,i+(some number of intervening
> nucleotides)."
>
> This is exactly what I meant, the linking. Is there a way to achieve this
> without messing with the code? I just haven't looked at the code, so
> if you think I'm being a cheeky little bastard, I'll accept that. :)
>
> Thanks,
>
> Alex
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and periodic molecule

[Alex]

Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem...

Thanks,

Alex





>


Hi Alex,
I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA
ACGT
You would generate 
TACGTA
Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a bit cumbersome, but this ensures all the links are correct and the modifications of the termini have no effect, and it's not very hard to script. And, of course, scripting it is a one time effort to avoid doing it manually later.
Cheers,
Tsjerk
On Apr 26, 2015 5:55 AM, "Alex"  wrote:

JL> The force field parameters for a phosphodiester are the same in a linear, finite
JL> DNA as they will be in your infinite chain.

I didn't mean that anything would need to be changed in the description of residues. The FF handles a
finite chain perfectly.

JL> The problem is in telling pdb2gmx
JL> "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)."

This is exactly what I meant, the linking. Is there a way to achieve this
without messing with the code? I just haven't looked at the code, so
if you think I'm being a cheeky little bastard, I'll accept that. :)

Thanks,

Alex


--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.








-- 
Best regards,
 Alex                            mailto:nedoma...@gmail.com



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx warning residue mapping

[Justin Lemkul]

On 7/1/15 2:13 PM, Nikhil wrote:

Dear all,
when i run pdb2gmx -f name.pdb with charmm27 and tip3 water model for my
structure i got an warning:
  Residue 1 named GLN of a molecule in the input file was mapped to an
entry in the topology database,but the atom CA used in that entry is not
found in the input file.Perhaps your atom and reside naming needs to be
fixed.

when i  checked my structure for four or five times i couldnt find any
problem atom CA which is defined in charmm27 still why this error.

how to solve this error or if i avoid and proceed it will make problem
during minimization and md?

here is GLN entry
ATOM   42   CD2  LEU A   6  -7.733  -2.176   0.996  1.00  0.00
C
ATOM   43   CA   GLN A   1  -3.232   3.298  -0.224  1.00  0.00
C
ATOM   44   CB   GLN A   1  -4.479   3.910   0.508  1.00  0.00
C
ATOM   45   CG   GLN A   1  -4.699   5.392   0.155  1.00  0.00
C
ATOM   46   CD   GLN A   1  -6.125   5.743   0.501  1.00  0.00
C
ATOM   47   NZ   GLN A   1  -6.625   7.021   0.232  1.00  0.00
N
ATOM   48   OD   GLN A   1  -6.886   4.863   0.922  1.00  0.00
O
ATOM   49   HN   GLN A   1  -2.342   1.326   0.325  1.00  0.00
H
ATOM   50   HN   LEU A   2  -1.012   3.459  -1.579  1.00  0.00
H
ATOM   51   HN   LYS A   3   0.953   2.002  -0.768  1.00  0.00
H
ATOM   52   HN   ALA A   4   1.202  -0.067  -0.562  1.00  0.00
H
ATOM   53   HN   LEU A   6  -2.606  -0.728   0.937  1.00  0.00
H
ATOM   54   HN   LYS A   5  -0.672  -1.114   0.652  1.00  0.00
H
ATOM   55   HA   LEU A   2   0.683   5.077  -1.474  1.00  0.00
H



You're missing all kinds of atoms.  This coordinate file is pretty hopeless.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx ffG43a1 force field

[Justin Lemkul]

On 10/16/14 10:55 PM, Nilesh Dhumal wrote:

Hello,

I am generating .top file using pdb2gmx and choose ffG43a1 force field
from the list.

pdb2gmx is running for an hour. Here I pasted the last part appeared on
screen

Select the Force Field:
  0: GROMOS96 43a1 force field
  1: GROMOS96 43a2 force field (improved alkane dihedrals)
  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
  6: [DEPRECATED] Gromacs force field (see manual)
  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
  8: Encad all-atom force field, using scaled-down vacuum charges
  9: Encad all-atom force field, using full solvent charges
0
Opening library file /usr/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
  this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
  this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading cu.gro...
Read 'Title', 156 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 156 atoms

   chain  #res #atoms
   1 '-' 1156

No occupancies in cu.gro
Opening library file /usr/share/gromacs/top/ffG43a1.atp
Atomtype 1
Cu


Could any one tell why is it taking so long time.

Total number of atom are 156 in system.



And they're all in one residue - what is in the coordinate file?  There's no 
reason for pdb2gmx to run that long; it's clearly stuck on something bizarre in 
your input file that it can't resolve.  Have you modified the force field in any 
way?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx ffG43a1 force field

[Justin Lemkul]

On 10/17/14 4:09 PM, Nilesh Dhumal wrote:

Hello,

I am generating .top file using pdb2gmx and choose ffG43a1 force field
from the list.

pdb2gmx is running for an hour. Here I pasted the last part appeared on
screen

Select the Force Field:
  0: GROMOS96 43a1 force field
  1: GROMOS96 43a2 force field (improved alkane dihedrals)
  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
  6: [DEPRECATED] Gromacs force field (see manual)
  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
  8: Encad all-atom force field, using scaled-down vacuum charges
  9: Encad all-atom force field, using full solvent charges
0
Opening library file /usr/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
  this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
  this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading cu.gro...
Read 'Title', 156 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 156 atoms

   chain  #res #atoms
   1 '-' 1156

No occupancies in cu.gro
Opening library file /usr/share/gromacs/top/ffG43a1.atp
Atomtype 1
Cu


Could any one tell why is it taking so long time.

Total number of atom are 156 in system.



Please see my reply from earlier to this same post:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092984.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx ffG43a1 force field

[Nilesh Dhumal]

All are from same residue.

I added following part in .rtp file.

[ BTC ]
  [ atoms ]
  Cu  Cu  1.0980
  OA   O  -0.665   0
  OB   O  -0.665   0
  CA   C   0.778   0
  CB   C  -0.092   0
  CC   C  -0.014   0
  HM   H   0.109   0
 [ bonds ]
 Cu   OA  gb_101
 Cu   OB  gb_101
 OA   CA  gb_102
 OB   CA  gb_102
 CA   CB  gb_103
 CB   CC  gb_104
 CC   HM  gb_105
 [ angles ]
 OA   Cu   OA   ga_101
 OB   Cu   OB   ga_101
 OA   Cu   OB   ga_102
 Cu   OA   CA   ga_103
 Cu   OB   CA   ga_103
 OA   CA   OA   ga_104
 OB   CA   OB   ga_104
 OA   CA   OB   ga_105
 OA   CA   CB   ga_106
 OB   CA   CB   ga_106
 CA   CB   CC   ga_107
 CC   CB   CC   ga_108
 CB   CC   CB   ga_109
 CB   CC   HM   ga_110
 [ impropers ]
;  aiajakal   gromos type
HMCC   CB   CB   gd_103
CACB   CC   CC   gd_104
CBCA   OA   OB   gd_104
CBCA   OB   OA   gd_104

 [ dihedrals ]
;  aiajakal   gromos type
 CuOA   CA   CB  gd_101
 CuOB   CA   CB  gd_101
 CuOA   CA   OB  gd_101
 CuOB   CA   OA  gd_101
 CuOA   CA   OA  gd_101
 CuOB   CA   OB  gd_101
 CBCC   CB   CC  gd_101
 CACB   CC   CB  gd_101
 CACB   CC   HM  gd_101
 CCCB   CC   HM  gd_101
 OACA   CB   CC  gd_102
 OBCA   CB   CC  gd_102




>
> On 10/17/14 4:09 PM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am generating .top file using pdb2gmx and choose ffG43a1 force field
>> from the list.
>>
>> pdb2gmx is running for an hour. Here I pasted the last part appeared on
>> screen
>>
>> Select the Force Field:
>>   0: GROMOS96 43a1 force field
>>   1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>   2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>   3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>   4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>   5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>   6: [DEPRECATED] Gromacs force field (see manual)
>>   7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>   8: Encad all-atom force field, using scaled-down vacuum charges
>>   9: Encad all-atom force field, using full solvent charges
>> 0
>> Opening library file /usr/share/gromacs/top/ffG43a1.rtp
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> WARNING: masses will be determined based on residue and atom names,
>>   this can deviate from the real mass of the atom type
>> Opening library file /usr/share/gromacs/top/atommass.dat
>> Entries in atommass.dat: 178
>> WARNING: vdwradii will be determined based on residue and atom names,
>>   this can deviate from the real mass of the atom type
>> Opening library file /usr/share/gromacs/top/vdwradii.dat
>> Entries in vdwradii.dat: 28
>> Opening library file /usr/share/gromacs/top/dgsolv.dat
>> Entries in dgsolv.dat: 7
>> Opening library file /usr/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file /usr/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Reading cu.gro...
>> Read 'Title', 156 atoms
>> Opening library file /usr/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>> There are 1 chains and 0 blocks of water and 1 residues with 156 atoms
>>
>>chain  #res #atoms
>>1 '-' 1156
>>
>> No occupancies in cu.gro
>> Opening library file /usr/share/gromacs/top/ffG43a1.atp
>> Atomtype 1
>> Cu
>>
>>
>> Could any one tell why is it taking so long time.
>>
>> Total number of atom are 156 in system.
>>
>
> Please see my reply from earlier to this same post:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092984.html
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.
>


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx ffG43a1 force field

[Justin Lemkul]

On 10/17/14 4:53 PM, Nilesh Dhumal wrote:

All are from same residue.

I added following part in .rtp file.

[ BTC ]
   [ atoms ]
   Cu  Cu  1.0980
   OA   O  -0.665   0
   OB   O  -0.665   0
   CA   C   0.778   0
   CB   C  -0.092   0
   CC   C  -0.014   0
   HM   H   0.109   0
  [ bonds ]
  Cu   OA  gb_101
  Cu   OB  gb_101
  OA   CA  gb_102
  OB   CA  gb_102
  CA   CB  gb_103
  CB   CC  gb_104
  CC   HM  gb_105
  [ angles ]
  OA   Cu   OA   ga_101
  OB   Cu   OB   ga_101
  OA   Cu   OB   ga_102
  Cu   OA   CA   ga_103
  Cu   OB   CA   ga_103
  OA   CA   OA   ga_104
  OB   CA   OB   ga_104
  OA   CA   OB   ga_105
  OA   CA   CB   ga_106
  OB   CA   CB   ga_106
  CA   CB   CC   ga_107
  CC   CB   CC   ga_108
  CB   CC   CB   ga_109
  CB   CC   HM   ga_110
  [ impropers ]
;  aiajakal   gromos type
HMCC   CB   CB   gd_103
CACB   CC   CC   gd_104
CBCA   OA   OB   gd_104
CBCA   OB   OA   gd_104

  [ dihedrals ]
;  aiajakal   gromos type
  CuOA   CA   CB  gd_101
  CuOB   CA   CB  gd_101
  CuOA   CA   OB  gd_101
  CuOB   CA   OA  gd_101
  CuOA   CA   OA  gd_101
  CuOB   CA   OB  gd_101
  CBCC   CB   CC  gd_101
  CACB   CC   CB  gd_101
  CACB   CC   HM  gd_101
  CCCB   CC   HM  gd_101
  OACA   CB   CC  gd_102
  OBCA   CB   CC  gd_102



If this is the case, your input file doesn't make any sense.  You've defined a 
single BTC residue has having 7 atoms, but your input file specifies one residue 
with 156 atoms.  Given that 156 is not evenly divisible by 7, something is wrong 
either in the .rtp or the input coordinates.


You'll need to describe in much greater detail what exactly you're working on, 
and provide (at least) your coordinate file for download.


-Justin







On 10/17/14 4:09 PM, Nilesh Dhumal wrote:

Hello,

I am generating .top file using pdb2gmx and choose ffG43a1 force field
from the list.

pdb2gmx is running for an hour. Here I pasted the last part appeared on
screen

Select the Force Field:
   0: GROMOS96 43a1 force field
   1: GROMOS96 43a2 force field (improved alkane dihedrals)
   2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
   3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
   4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
   5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
   6: [DEPRECATED] Gromacs force field (see manual)
   7: [DEPRECATED] Gromacs force field with hydrogens for NMR
   8: Encad all-atom force field, using scaled-down vacuum charges
   9: Encad all-atom force field, using full solvent charges
0
Opening library file /usr/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
   this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
   this can deviate from the real mass of the atom type
Opening library file /usr/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading cu.gro...
Read 'Title', 156 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 156 atoms

chain  #res #atoms
1 '-' 1156

No occupancies in cu.gro
Opening library file /usr/share/gromacs/top/ffG43a1.atp
Atomtype 1
Cu


Could any one tell why is it taking so long time.

Total number of atom are 156 in system.



Please see my reply from earlier to this same post:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092984.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-requ...@gromacs.org.






--
===

Re: [gmx-users] pdb2gmx atom not found

[Justin Lemkul]

On 12/12/14 12:52 PM, xy21hb wrote:

Dear all,


I am introducing a residue named ABC into AMBER03 force field. I built up the 
aminoacids.rtp and aminoacids.hdb file,
but when I pdb2gmx, it gives,
"
Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB
"
I am pretty sure I use HB instead of HB1, and there is no atom called HB1 in 
any of the above-mentioned files.(including .pdb for pdb2gmx)
then I changed my HB to HB1, it gives similar error,


"
Atom HB11 not found in rtp database in residue ABC, it looks a bit like HB1
"


It seems that pdb2gmx is appending the name with "1".


Anyone knows why that is?



Probably due to the .hdb entry - if multiple H are to be built on a single heavy 
atom, numbers are appended so they have unique names.  But to take the guesswork 
out, you'll need to provide the exact text of the .rtp and .hdb files.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx command not found

[Dallas Warren]

Versions of GROMACS for awhile now have moved all the scripts underneath
"gmx". So now you need use "gmx pdb2gmx"

On Fri, 20 Mar. 2020, 5:28 am Sutanu L'Étranger, <
schrodingerscat...@gmail.com> wrote:

> Hi,
>
> I've recently installed gromacs latest version, but when I type pdb2gmx, it
> shows "pdb2gmx command not found", please advise. Thank you.
>
> Regards,
> Sutanu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx, charmm22 and HEME

[Justin Lemkul]

On 4/29/14, 5:13 PM, Erik Marklund wrote:

Dear users,

I am trying to preprocess a cytochrome C structure with pdb2gmx and have run 
into some problems. The forcefield has parameters for the HEME group, but other 
components are missing to successfully produce the topology etc. First of all, 
the hdb files don't have an entry for HEME, but I managed to make one myself 
(which I am happy to share with the gromacs community). What's worse however, 
is that the histidine that sits bang on top of the Fe in the HEME is turned 
into a HIS1, which isn't found in the ftp files:

...
Linking CYS-14 SG-109 and HEM-105 CAB-845...
Linking CYS-17 SG-129 and HEM-105 CAC-853...
Linking HIS-18 NE2-139 and HEM-105 FE-866...
Linking MET-80 SD-626 and HEM-105 FE-866...

---
Program pdb2gmx, VERSION 4.6.6-dev-20131203-a2e1958-unknown
Source code file: 
/u/jlpb/marklund/src/gmx/release-4-6/gromacs/src/kernel/resall.c, line: 642

Fatal error:
Residue 'HIS1' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

How do I resolve this issue? This has been discussed in the mailing list 
before, but so far I've only found dead ends



The HIS1 nomenclature is tailored to Gromos and OPLS, both of which declare a 
special HIS1 residue in the .rtp that is a clone of HIS-delta (HISA in Gromos). 
 For CHARMM, the equivalent would be to declare HSD as the ligating residue. 
Presumably, replacing HIS1 with HSD in specbond.dat (a local copy should 
override the one in $GMXLIB) will fix this.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx, charmm22 and HEME

[Erik Marklund]

On 29 Apr 2014, at 23:32, Justin Lemkul  wrote:

> 
> 
> On 4/29/14, 5:13 PM, Erik Marklund wrote:
>> Dear users,
>> 
>> I am trying to preprocess a cytochrome C structure with pdb2gmx and have run 
>> into some problems. The forcefield has parameters for the HEME group, but 
>> other components are missing to successfully produce the topology etc. First 
>> of all, the hdb files don't have an entry for HEME, but I managed to make 
>> one myself (which I am happy to share with the gromacs community). What's 
>> worse however, is that the histidine that sits bang on top of the Fe in the 
>> HEME is turned into a HIS1, which isn't found in the ftp files:
>> 
>> ...
>> Linking CYS-14 SG-109 and HEM-105 CAB-845...
>> Linking CYS-17 SG-129 and HEM-105 CAC-853...
>> Linking HIS-18 NE2-139 and HEM-105 FE-866...
>> Linking MET-80 SD-626 and HEM-105 FE-866...
>> 
>> ---
>> Program pdb2gmx, VERSION 4.6.6-dev-20131203-a2e1958-unknown
>> Source code file: 
>> /u/jlpb/marklund/src/gmx/release-4-6/gromacs/src/kernel/resall.c, line: 642
>> 
>> Fatal error:
>> Residue 'HIS1' not found in residue topology database
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>> 
>> How do I resolve this issue? This has been discussed in the mailing list 
>> before, but so far I've only found dead ends
>> 
> 
> The HIS1 nomenclature is tailored to Gromos and OPLS, both of which declare a 
> special HIS1 residue in the .rtp that is a clone of HIS-delta (HISA in 
> Gromos).  For CHARMM, the equivalent would be to declare HSD as the ligating 
> residue. Presumably, replacing HIS1 with HSD in specbond.dat (a local copy 
> should override the one in $GMXLIB) will fix this.
> 
> -Justin
> 

Thanks a million. Worked like a charm (no pun intended).

Erik

> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and the Glu residue

[Justin Lemkul]

On 4/25/15 10:40 AM, Brett wrote:

Dear All,

In the top file produced by H++ server for AMBER, if there is no charge for the 
Glu, the residue name will be modified to GLH. In our gromacs, we never treat 
Glu as without charge, thus we do not have GLH residue, am I right?



No.  You can treat glutamate however you like (and in this case, it sounds like 
it should be protonated).  Different force fields call the residue different 
things.  It's GLH in AMBER force fields, GLUH in GROMOS and OPLS-AA, and GLUP in 
CHARMM.  Thus, all the force fields support the protonated form.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and the terminal residue

[Justin Lemkul]

On 4/25/15 10:49 AM, Brett wrote:

Dear All,

For the pdb2gmx, if I will not assign charges to the N-terminal residue and 
C-terminal residue, I need to use pdb2gmx -ter, or I need to use pdb2gmx 
-[no]ter?



The -ter option allows you to choose protonation state or no terminal processing 
if there are caps.



In addition, whether there will be charges at the  N-terminal residue and 
C-terminal residue has relation with the force field used,  am I right?



I don't understand this question.  The individual partial charges on the atoms 
are indeed a function of the force field, but the choice of protonation state or 
capping is totally independent of the force field and is dictated by biological 
relevance.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

[David van der Spoel]

On 28/01/16 08:33, Md. Imrul Reza Shishir wrote:

Hi Everyone.
I use Lenovo A6-7310 (4 core 2MB cache memory) processor in my laptop. I
install Gromacs 5.0.7 with latest cmake-3.4.2 and fftw-3.3.4. I use below
Cmake command to install.

"cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON"

I am newbies gromacs user. I am trying to execute the Bevan Lab tutorial
(Lysozyme in water). my first command is

"gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce"

It execute properly. But when i execute number 15 force
field(OPLS-AA/L) at the end there is a massage "illegal instruction
(core dumped)". And in my directory only topology file create. No
gromacs output file Created "1AKI_processed.gro".

Illegal instruction means the program was compiled for another machine 
than what it is run on. Did you really compile the program on the same 
machine you are running on?


In that case you may need to manually set the GMX_SIMD flag when running 
cmake, e.g.

-DGMX_SIMD=SSE4.1



Any help greatly appreciated.

​Bst Regards​




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

[Md. Imrul Reza Shishir]

Thank you David van der Spoel. I compile gromacs in my own laptop and I run
on the same machine. Your guideline working properly. I reinstall gromacs
and now all okk..

regards and thank you.

Md Imrul Reza Shishir
On Jan 28, 2016 4:47 PM, "David van der Spoel"  wrote:

> On 28/01/16 08:33, Md. Imrul Reza Shishir wrote:
>
>> Hi Everyone.
>> I use Lenovo A6-7310 (4 core 2MB cache memory) processor in my laptop. I
>> install Gromacs 5.0.7 with latest cmake-3.4.2 and fftw-3.3.4. I use below
>> Cmake command to install.
>>
>> "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON"
>>
>> I am newbies gromacs user. I am trying to execute the Bevan Lab tutorial
>> (Lysozyme in water). my first command is
>>
>> "gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce"
>>
>> It execute properly. But when i execute number 15 force
>> field(OPLS-AA/L) at the end there is a massage "illegal instruction
>> (core dumped)". And in my directory only topology file create. No
>> gromacs output file Created "1AKI_processed.gro".
>>
>> Illegal instruction means the program was compiled for another machine
> than what it is run on. Did you really compile the program on the same
> machine you are running on?
>
> In that case you may need to manually set the GMX_SIMD flag when running
> cmake, e.g.
> -DGMX_SIMD=SSE4.1
>
>
> Any help greatly appreciated.
>>
>> ​Bst Regards​
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx disulfide bond in dimer

[Justin Lemkul]

On 4/14/16 6:32 AM, s.varriale wrote:


Dear all,
I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4.
I do:
pdb2gmx -f prot.pdb -chainsep ter
and the programme generates a .gro file with disulfide bond.
but when i want to minimize the system, there is an error:

There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is larger
than the 1-4 table size 2.200 nm

if I try to simulate the 2 chains separatly, there is any error.
What can i do?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx disulfide bond in dimer

[s.varriale]

thank you Justin, but I can't understand how to solve my  problem.
when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique 
chain because  N- and C- termini of 2 chains are linked.


Sonia
Il 14/04/2016 13:46 Justin Lemkul ha scritto:

On 4/14/16 6:32 AM, s.varriale wrote:


Dear all,
I try to perform a MD simulation of a covalent dimer with gromacs 
4.5.4.

I do:
pdb2gmx -f prot.pdb -chainsep ter
and the programme generates a .gro file with disulfide bond.
but when i want to minimize the system, there is an error:

There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is 
larger

than the 1-4 table size 2.200 nm

if I try to simulate the 2 chains separatly, there is any error.
What can i do?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


--
Sonia Varriale, PhD
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx disulfide bond in dimer

[Justin Lemkul]

On 4/14/16 9:53 AM, s.varriale wrote:

thank you Justin, but I can't understand how to solve my  problem.
when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique chain
because  N- and C- termini of 2 chains are linked.



As it should.  The two chains have to be merged into a single [moleculetype] 
definition for that bond to be created.  The merging process isn't causing 
stability; some other aspect of your structure is.  The link I provided includes 
all the usual diagnostic information.  Unless you go through those steps (and 
have a look through some of the other million or so posts regarding the same 
issue) and provide some more useful details about what you observe, there's 
little anyone else can suggest.


-Justin


Sonia
Il 14/04/2016 13:46 Justin Lemkul ha scritto:

On 4/14/16 6:32 AM, s.varriale wrote:


Dear all,
I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4.
I do:
pdb2gmx -f prot.pdb -chainsep ter
and the programme generates a .gro file with disulfide bond.
but when i want to minimize the system, there is an error:

There were 2 inconsistent shifts. Check your topology
Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is larger
than the 1-4 table size 2.200 nm

if I try to simulate the 2 chains separatly, there is any error.
What can i do?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and specbond with arbitrary ligand

[Justin Lemkul]

On 3/11/15 1:08 PM, Leandro Bortot wrote:

Dear users,

  I want to simulate some ligands covalently bonded to a protein, i.e.
covalent inhibitors. I've searched the list and found similar issues, but
mainly with heme in forcefields in which it is already supported. I use the
AMBER99SB-ILDN forcefield and I can simulate the non covalent complexes
with no problems using GAFF.

  I suppose I can just put both the ligand and the protein under the
same [moleculetype] specification in a .itp file and manually add the bonds
in this topology. It seems that I only need a script to renumber the atoms
to achieve this. However, I think pdb2gmx and specbond.dat may already be
able to do this. The problem is: How can pdb2gmx understand my arbitrary
ligand? Is adding my ligand to a local copy of
amber99sb-ildn/aminoacids.rtp the only way?

  What would be the best way to do that?



Yes, the .rtp approach is the most reliable way to do this.  Follow all the 
steps in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
and add an entry in specbond.dat (format explained in 
http://www.gromacs.org/Documentation/File_Formats/specbond.dat)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx and specbond with arbitrary ligand

[Leandro Bortot]

Hi,

 Thank you Justin. I added the ligand to the forcefield as a new
residue by editing local copies of aminoacids.rtp, atomtypes.atp,
ffbonded.itp and ffnonbonded.itp using information from the .itp for the
isolated ligand I already had. Additionally, I created the protein-ligand
bonds using specbond.dat. Everything worked well.





 For the sake of helping others who may encounter similar situations, I
report two things I didn't expect:


 First: ffbonded.itp is not case sensitive. I had the new atom types
"c" and "o" and grompp gave me the following warnings:

"











*WARNING 1 [file ffbonded.itp, line 116]:  Overriding Bond parameters.
old:  0.1229 476976 0.1229 476976
new: c   o10.12140   542250.0WARNING 2 [file ffbonded.itp, line
404]:  Overriding Angle parameters.
old:  126 669.44 126 669.44   new:
oco   1130.380654.130*
"

 The old values are the parameters for the the "C O" bond and "O C O
" angles, which are conflicting with the new "c o" bond and "o c o" angle.
I solved this by renaming "c" and "o" to something else, but I didn't
expected this to happen since ffnonbonded.itp is case sensitive.



 Second: the AMBER99SB-ILDN forcefield uses the dihedral function 9 for
propers and function 4 for impropers. On the other hand, the
parametrization by GAFF/Antechamber/acpype uses function 3 for propers and
function 1 for impropers. The problem is that pdb2gmx seems to assume that
all proper dihedrals use function 9 and impropers use function 4, including
the ligand ones. As a result, grompp give many "No default Proper Dih.
types" and "No default Improper Dih. types" errors. Since the ligand is in
the end of the chain .itp file that pdb2gmx created, this is easily fixed
by renumbering the adequate dihedral functions in a text editor.




Thank you for your attention,
Leandro.



On Wed, Mar 11, 2015 at 10:20 PM, Justin Lemkul  wrote:

>
>
> On 3/11/15 1:08 PM, Leandro Bortot wrote:
>
>> Dear users,
>>
>>   I want to simulate some ligands covalently bonded to a protein, i.e.
>> covalent inhibitors. I've searched the list and found similar issues, but
>> mainly with heme in forcefields in which it is already supported. I use
>> the
>> AMBER99SB-ILDN forcefield and I can simulate the non covalent complexes
>> with no problems using GAFF.
>>
>>   I suppose I can just put both the ligand and the protein under the
>> same [moleculetype] specification in a .itp file and manually add the
>> bonds
>> in this topology. It seems that I only need a script to renumber the atoms
>> to achieve this. However, I think pdb2gmx and specbond.dat may already be
>> able to do this. The problem is: How can pdb2gmx understand my arbitrary
>> ligand? Is adding my ligand to a local copy of
>> amber99sb-ildn/aminoacids.rtp the only way?
>>
>>   What would be the best way to do that?
>>
>>
> Yes, the .rtp approach is the most reliable way to do this.  Follow all
> the steps in http://www.gromacs.org/Documentation/How-tos/Adding_
> a_Residue_to_a_Force_Field and add an entry in specbond.dat (format
> explained in http://www.gromacs.org/Documentation/File_Formats/
> specbond.dat)
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx on HID HIE and HIP

[Justin Lemkul]

On 4/25/15 5:35 AM, Brett wrote:

Dear All,

Will you please tell me which software or server can handle a PDB file so that 
the HIS residues in the original PDB file will be automatically changed into 
HID, HIE and HIP in the new PDB file, which can be processed by pdb2gmx, based 
on the H patten in the HIS residues in the original PDB file?



Does "H pattern" mean the actual atoms or the hydrogen bonding network.  If the 
former, that means you already have the H atoms built and you just need to 
change the residue names.  If the latter, that's exactly what pdb2gmx does.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error after switching force fields

[Justin Lemkul]

On 5/13/16 10:49 AM, Irem Altan wrote:

Hi,

I have a .pdb file that I’ve used in simulations with amber99sb before. I have 
recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
ago, so you're using something really outdated :)



The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
85, 95). The weird thing is, the residue numbers in the pdb file start from 
107, and gmx complains about lower numbers. Also, have I understood correctly 
that gmx complains that glycines in my input file don’t have beta carbons? What 
could be the problem here?



pdb2gmx uses its own internal numbering, starting from 1.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error after switching force fields

[Irem Altan]

Hi,

Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually 
using Gromacs 5.1.2.

Best,
Irem

> On May 13, 2016, at 10:52 AM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/13/16 10:49 AM, Irem Altan wrote:
>> Hi,
>> 
>> I have a .pdb file that I’ve used in simulations with amber99sb before. I 
>> have recently switched to amber03. When I do pdb2gmx, I get the following 
>> warning:
>> 
>> WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom CB used in
>> an interaction of type dihedral in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>> 
> 
> There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
> calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
> ago, so you're using something really outdated :)
> 
>> The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
>> 85, 95). The weird thing is, the residue numbers in the pdb file start from 
>> 107, and gmx complains about lower numbers. Also, have I understood 
>> correctly that gmx complains that glycines in my input file don’t have beta 
>> carbons? What could be the problem here?
>> 
> 
> pdb2gmx uses its own internal numbering, starting from 1.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx error after switching force fields

[Justin Lemkul]

On 5/13/16 11:04 AM, Irem Altan wrote:

Hi,

Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually 
using Gromacs 5.1.2.



Not sure how that's possible.  It should have been fixed prior to the release of 
5.1.1.


-Justin


Best,
Irem


On May 13, 2016, at 10:52 AM, Justin Lemkul  wrote:



On 5/13/16 10:49 AM, Irem Altan wrote:

Hi,

I have a .pdb file that I’ve used in simulations with amber99sb before. I have 
recently switched to amber03. When I do pdb2gmx, I get the following warning:

WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
ago, so you're using something really outdated :)


The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 
85, 95). The weird thing is, the residue numbers in the pdb file start from 
107, and gmx complains about lower numbers. Also, have I understood correctly 
that gmx complains that glycines in my input file don’t have beta carbons? What 
could be the problem here?



pdb2gmx uses its own internal numbering, starting from 1.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx vsites error reading atom name

[Sotirios Dionysios I. Papadatos]

Maybe you are trying to simulate a molecule that is not mentioned in the 
aminoacids.rtp on the force field of your choice or more probably the atom that 
is mentioned on the error report has a different name than the the one provided 
on the pdb file.

My advice is to check on the ff directory > aminoacids.rtp the molecule name 
and see the atom names that it needs.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Vasiliu Tudor 

Sent: Tuesday, December 6, 2016 3:29:19 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] pdb2gmx vsites error reading atom name

Hello I was wondering if someone has any idee as to what is happening with my 
.gro file.These are the first 3 atoms in my .gro file
1URE10C1   0.570   0.517   0.272
1URE11C2   0.555   0.365   0.285
1URE12C3   0.505   0.592   0.388now these are the first 3 atoms in 
the .rtp file[ URE ]
 [ atoms ]
 10CCG311   0.045   1
 11CCG321   0.037   1
 12CCG321   0.037   1
when I run the pdb2gmx command: echo '1' | pdb2gmx -f Uree.1.gro -vsite 
hydrogens -water tip3p -o vsUree.0.gro -p Uree.topI get the following error : 
Fatal error:
Atom 0C1 in residue URE 1 was not found in rtp entry URE with 43 atoms
while sorting atoms.
can someone pls tell my why gromacs see's the first atom as 0C1 instead of 10C? 
P.S. If I load the .gro file in VMD the name of the first atom is 10C and if I 
change in the .rtp 10C to 0C1 it works and asks for atom 1C1 and so on
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx: how to preserve original ions?

[Justin Lemkul]

On 7/17/18 9:22 PM, Anderson, Amos wrote:

Hi Gromacs users,

I’ve never used gromacs before, so sorry if this question has an obvious answer 
somewhere — it seems like the sort I should have been able to find an answer 
for…

I want to write a python script to prepare an arbitrary pdb for use with gromacs 
(e.g., does these steps http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for 
the user). The input pdb to my script may have waters, ions, and ligand(s) in it 
already. In the tutorial it says "you are going to want to strip out the 
crystal waters, PO4, and BME. Note that such a procedure is not universally 
appropriate (i.e., the case of a bound active site water molecule).” The wording 
maybe implies that other than active site waters and the ligand of interest, I’d 
never want to preserve HETATOMs in my input file?

If not, and if I do want to keep them, how do I? Do I just treat all of them 
like ligands in the tutorial, e.g., maybe a protocol like this (more precise 
for ions I care about)?

  *   grep HETATOM my.pdb > hetatoms.pdb


HETATM, but yes.


  *   gmx editconf -f hetatoms.pdb -o hetatoms.gro
  *   copy/paste hetatoms.gro into my main .gro file (is there 
python/utility anywhere for merging .gro files I could leverage?)


Conversion to .gro format is unnecessary; GROMACS handles PDB and other 
formats, if you prefer.



  *   for ions gromacs doesn’t already know about (ions.itp), follow the 
instructions described here: 
http://www.mdtutorials.com/gmx/complex/02_topology.html


Parametrization servers won't generally deal with monoatomic species. In 
a pairwise additive force field, the charge is already fixed and LJ have 
to be tuned, typically based on free energy of solvation.



(in other words, I’m puzzled why pdb2gmx is complaining about ions it should 
already know about from the built-in ions.itp)


pdb2gmx doesn't know anything about ions.itp, that comes in later when 
calling grompp. pdb2gmx only knows about what is defined in the force 
field .rtp file(s).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx: how to preserve original ions?

[Mark Abraham]

Hi,

The name of the residue in that force fields aminoacids.rtp is CLA, which
is the only thing pdb2gmx can understand. Otherwise your procedure should
just work if you rename your ion residues appropriately. Do let us know how
you go!

Mark

On Wed, Jul 18, 2018, 03:23 Anderson, Amos  wrote:

> Hi Gromacs users,
>
> I’ve never used gromacs before, so sorry if this question has an obvious
> answer somewhere — it seems like the sort I should have been able to find
> an answer for…
>
> I want to write a python script to prepare an arbitrary pdb for use with
> gromacs (e.g., does these steps
> http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The
> input pdb to my script may have waters, ions, and ligand(s) in it already.
> In the tutorial it says "you are going to want to strip out the crystal
> waters, PO4, and BME. Note that such a procedure is not universally
> appropriate (i.e., the case of a bound active site water molecule).” The
> wording maybe implies that other than active site waters and the ligand of
> interest, I’d never want to preserve HETATOMs in my input file?
>
> If not, and if I do want to keep them, how do I? Do I just treat all of
> them like ligands in the tutorial, e.g., maybe a protocol like this (more
> precise for ions I care about)?
>
>  *   grep HETATOM my.pdb > hetatoms.pdb
>  *   gmx editconf -f hetatoms.pdb -o hetatoms.gro
>  *   copy/paste hetatoms.gro into my main .gro file (is there
> python/utility anywhere for merging .gro files I could leverage?)
>  *   for ions gromacs doesn’t already know about (ions.itp), follow
> the instructions described here:
> http://www.mdtutorials.com/gmx/complex/02_topology.html
>
> (in other words, I’m puzzled why pdb2gmx is complaining about ions it
> should already know about from the built-in ions.itp)
>
> Thanks for any advice,
> Amos.
>
>
>
> To help future googlers, I run pdb2gmx on a file that has CL in it like
> this:
>
>
> gmx_d pdb2gmx -v -o output.gro -p output.top -ignh -water tip3p -ff
> charmm27 -f my.pdb
>
>  I get this error:
>
>
> Program: gmx pdb2gmx, version 2016.3
> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)
>
> Fatal error:
> Residue 'CL' not found in residue topology database
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> which surprises me because CL is defined in ions.itp. It says it’s finding
> other files in the same directory as ions.itp, so it doesn’t seem like some
> kind of misconfigured software install.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx: how to preserve original ions?

[Anderson, Amos]

uot;]

 found = False
 for k,v in options.items():
if v == selectedOption:
   found = True
   print("# Selecting terminal option %s:%s for residue 
%s"%(v,k,resname))
         if not found: print("Unknown option but trying anyway:",selectedOption)
 p.sendline(selectedOption)


  except pexpect.EOF:
 print(p.before)
  except pexpect.TIMEOUT:
 print("TIMEOUT")
 print(p.before)

   os.chdir(origDir)
   runCmdsAndZipResults([],dirname)
   print("\n\n# Done making Gromacs files...\n\n")






Message: 2
Date: Tue, 17 Jul 2018 21:26:11 -0400
From: Justin Lemkul mailto:jalem...@vt.edu>>
To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] pdb2gmx: how to preserve original ions?
Message-ID: 
mailto:dba7c125-0f3b-0a16-0d85-f0dd054b4...@vt.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 7/17/18 9:22 PM, Anderson, Amos wrote:
Hi Gromacs users,

I?ve never used gromacs before, so sorry if this question has an obvious answer 
somewhere ? it seems like the sort I should have been able to find an answer 
for?

I want to write a python script to prepare an arbitrary pdb for use with 
gromacs (e.g., does these steps 
http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The input 
pdb to my script may have waters, ions, and ligand(s) in it already. In the 
tutorial it says "you are going to want to strip out the crystal waters, PO4, 
and BME. Note that such a procedure is not universally appropriate (i.e., the 
case of a bound active site water molecule).? The wording maybe implies that 
other than active site waters and the ligand of interest, I?d never want to 
preserve HETATOMs in my input file?

If not, and if I do want to keep them, how do I? Do I just treat all of them 
like ligands in the tutorial, e.g., maybe a protocol like this (more precise 
for ions I care about)?

   *   grep HETATOM my.pdb > hetatoms.pdb

HETATM, but yes.

   *   gmx editconf -f hetatoms.pdb -o hetatoms.gro
   *   copy/paste hetatoms.gro into my main .gro file (is there 
python/utility anywhere for merging .gro files I could leverage?)

Conversion to .gro format is unnecessary; GROMACS handles PDB and other
formats, if you prefer.

   *   for ions gromacs doesn?t already know about (ions.itp), follow the 
instructions described here: 
http://www.mdtutorials.com/gmx/complex/02_topology.html

Parametrization servers won't generally deal with monoatomic species. In
a pairwise additive force field, the charge is already fixed and LJ have
to be tuned, typically based on free energy of solvation.

(in other words, I?m puzzled why pdb2gmx is complaining about ions it should 
already know about from the built-in ions.itp)

pdb2gmx doesn't know anything about ions.itp, that comes in later when
calling grompp. pdb2gmx only knows about what is defined in the force
field .rtp file(s).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu<mailto:jalem...@vt.edu> | (540) 231-3129
http://www.thelemkullab.com

==






--

Message: 4
Date: Wed, 18 Jul 2018 08:31:00 +0200
From: Mark Abraham mailto:mark.j.abra...@gmail.com>>
To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Cc: 
"gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>"
mailto:gromacs.org_gmx-users@maillist.sys.kth.se>>
Subject: Re: [gmx-users] pdb2gmx: how to preserve original ions?
Message-ID:
mailto:camnumash_0j2owuujdv69+daxhqp7ecdsa01g_vscqv2ztf...@mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"

Hi,

The name of the residue in that force fields aminoacids.rtp is CLA, which
is the only thing pdb2gmx can understand. Otherwise your procedure should
just work if you rename your ion residues appropriately. Do let us know how
you go!

Mark

On Wed, Jul 18, 2018, 03:23 Anderson, Amos 
mailto:amos.ander...@pfizer.com>> wrote:

Hi Gromacs users,

I?ve never used gromacs before, so sorry if this question has an obvious
answer somewhere ? it seems like the sort I should have been able to find
an answer for?

I want to write a python script to prepare an arbitrary pdb for use with
gromacs (e.g., does these steps
http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The
input pdb to my script may have waters, ions, and ligand(s) in it already.
In the tutorial it says "you are going to want to strip out the crystal
waters, PO4, and BME. Note that such a procedure is not universally
appropriate (i.e., the case of a bound active site water molecule).? The
wording maybe implies that

Re: [gmx-users] pdb2gmx charmm issue with version 2018.3

[Justin Lemkul]

On 10/12/18 8:10 PM, Akshay wrote:

Hello All,

I have been using Gromacs version 2016 and upgraded this week to 2018.3. In
the new version, I am having an issue with pdb2gmx. My file is a series of
protein chains and finally a dna-double helix like the following

chain A - Protein
chain B - Protein
chain C - Protein
chain D - DNA
chain E - DNA

Running pdb2gmx using gromacs 2018.3 and choosing the charm27 ff, I get the
error message "atom N not found in building block 1DG while combining tdb
and rtp". Chains A-C are built correctly.  So, I guess it is looking for an
amino N-terminal in the DNA chain D as I see the message "Start terminus
DG-1169: NH3+"

The issue seems specific to the Charmm27 FF as the Amber FFs are working
fine. The issue was also not present with Charmm within the 2016.1 version
I was running until last week.


You need to interactively select termini for complex systems.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Mark Abraham]

Hi,

pdb2gmx has options that configure its behaviour to let you choose whether
PDB TER records and/or changes of chain ID should separate molecules, etc.
You could explore those, and/or perhaps add such TER records to make your
intent clearer to the tool. (But with incomplete information, I can't be
sure that will help...)

Mark

On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan 
wrote:

> Dear All,
>
> I have a very big system with 4 proteins and membrane system. The
> relevant topology part is as follows:
>
> [ molecules ]
> ; Compound#mols
> ANAA 1
> ANAC 1
> P11A 1
> P11C 1
> CHL1   190
> POPC   380
> DOPC   190
> POPI24  80
> POPS   160
> TIP3179172
> SOD770
> CLA351
> CAL 30
>
> The first four molecules are the proteins. Each of these molecules has
> CTER patch applied in CHARMM using charmm36 force field.
>
> During the convertion with pdb2gmx I get an error. Below are shown some
> relevant parts of the output:
>
> *Processing chain 1 (675703 atoms, 110937 residues)**
> **Identified residue MET1 as a starting terminus.**
> **Warning: Residue CHL11 in chain has different type (Other) from
> starting residue MET1 (Protein).**
> **Warning: Residue CHL12 in chain has different type (Other) from
> starting residue MET1 (Protein).**
> **Warning: Residue CHL13 in chain has different type (Other) from
> starting residue MET1 (Protein).**
> **Warning: Residue CHL14 in chain has different type (Other) from
> starting residue MET1 (Protein).**
> **Warning: Residue CHL15 in chain has different type (Other) from
> starting residue MET1 (Protein).**
> **More than 5 unidentified residues at end of chain - disabling further
> warnings.**
> **Identified residue LYS96 as a ending terminus.*
>
> Although there are warnings, however, the problem seems to be in another
> place. The next portion is the following:
>
> *Start terminus MET-1: NH3+**
> **End terminus LYS-96: COO-**
> **Opening force field file
>
> /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn**
> *
>  From the above one can see that the program only detected the CTER of
> the P11C molecule (it is 96 residues large) and missed the CTERS of
> ANAA, ANAC and P11A. And now comes the actual error:
>
> *Program gmx_5.0.4_mpi, VERSION 5.0.4**
> **Source code file:
> /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c,
> line: 732**
> **
> **Fatal error:**
> **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12
> atoms**
> **while sorting atoms.**
> *
> I guess the above error indicates that the pdb2gmx could not detect the
> CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears.
>
> Could someone suggest a resolution?
>
> Thanks a lot in advance.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Davit Hakobyan]

Thank you for the suggestion.

I have tried to use the "-ter" flagbut this does not helpsince the 
problem is not because pdb2gmx cannot recognize the C-terminal patch, 
but that it misses the termianals of the intermediate proteins.The 
protein sequence in my system is like:


ANAA,ANAC,P11A,P11C

So even when I use the "-ter" flag the program asks to specify the 
N-termianl patch for ANAA and C-terminal patch for P11C. But all the 
four molecules are independent chains and each of them have both 
N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them 
as a single long chain?


Thanks again for any help.
Davit


On 3/13/2017 5:54 PM, Mark Abraham wrote:

Hi,

pdb2gmx has options that configure its behaviour to let you choose whether
PDB TER records and/or changes of chain ID should separate molecules, etc.
You could explore those, and/or perhaps add such TER records to make your
intent clearer to the tool. (But with incomplete information, I can't be
sure that will help...)

Mark

On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan 
wrote:


Dear All,

I have a very big system with 4 proteins and membrane system. The
relevant topology part is as follows:

[ molecules ]
; Compound#mols
ANAA 1
ANAC 1
P11A 1
P11C 1
CHL1   190
POPC   380
DOPC   190
POPI24  80
POPS   160
TIP3179172
SOD770
CLA351
CAL 30

The first four molecules are the proteins. Each of these molecules has
CTER patch applied in CHARMM using charmm36 force field.

During the convertion with pdb2gmx I get an error. Below are shown some
relevant parts of the output:

*Processing chain 1 (675703 atoms, 110937 residues)**
**Identified residue MET1 as a starting terminus.**
**Warning: Residue CHL11 in chain has different type (Other) from
starting residue MET1 (Protein).**
**Warning: Residue CHL12 in chain has different type (Other) from
starting residue MET1 (Protein).**
**Warning: Residue CHL13 in chain has different type (Other) from
starting residue MET1 (Protein).**
**Warning: Residue CHL14 in chain has different type (Other) from
starting residue MET1 (Protein).**
**Warning: Residue CHL15 in chain has different type (Other) from
starting residue MET1 (Protein).**
**More than 5 unidentified residues at end of chain - disabling further
warnings.**
**Identified residue LYS96 as a ending terminus.*

Although there are warnings, however, the problem seems to be in another
place. The next portion is the following:

*Start terminus MET-1: NH3+**
**End terminus LYS-96: COO-**
**Opening force field file

/home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn**
*
  From the above one can see that the program only detected the CTER of
the P11C molecule (it is 96 residues large) and missed the CTERS of
ANAA, ANAC and P11A. And now comes the actual error:

*Program gmx_5.0.4_mpi, VERSION 5.0.4**
**Source code file:
/home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c,
line: 732**
**
**Fatal error:**
**Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12
atoms**
**while sorting atoms.**
*
I guess the above error indicates that the pdb2gmx could not detect the
CTER portion of ANAA/ANAC (their last residue is ASP) so the error appears.

Could someone suggest a resolution?

Thanks a lot in advance.
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.