Re: [gmx-users] pdb2gmx error

[Justin A. Lemkul]

Ilya Chorny wrote:
I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached 
to the side chain nitrogen called ASBG. I want to test the new residue 
by itself.


When I pdb2gmx it I get the following error.

---
Program pdb2gmx, VERSION 4.0.3
Source code file: pgutil.c, line: 87

Fatal error:
Atom N not found in residue 1094904186 while adding improper

---



If the residue is by itself, something is seriously wrong if pdb2gmx is 
detecting a billion residues!


If I comment out 


 CA+N C O improper_O_C_X_Y



Right, because if the residue is by itself, there will be no N in the next 
residue (+N).



Then pdb2gmx creates the gro and top with no error messages.

I saw an much earlier post by Justin with a similar error message but no 
resolution. Anyone have anythoughts?




IIRC, that was in reference to version 3.3.1, which turned out to be the result 
of a broken Ubuntu package, and was not a problem with Gromacs itself.


Try it in the context of the actual molecule, if topology construction requires 
the next residue.  In isolation, that residue will always fail with +N.


-Justin


Thanks,

Ilya




--
Ilya Chorny Ph.D.




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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] pdb2gmx error

[Ilya Chorny]

I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to
the side chain nitrogen called ASBG. I want to test the new residue by
itself.
When I pdb2gmx it I get the following error.

---
Program pdb2gmx, VERSION 4.0.3
Source code file: pgutil.c, line: 87

Fatal error:
Atom N not found in residue 1094904186 while adding improper

---

If I comment out

 CA+N C O improper_O_C_X_Y

Then pdb2gmx creates the gro and top with no error messages.

I saw an much earlier post by Justin with a similar error message but no
resolution. Anyone have anythoughts?

Thanks,

Ilya




-- 
Ilya Chorny Ph.D.
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Re: [gmx-users] how to parametrize Phos. Thr TPO

[Lucio Ricardo Montero Valenzuela]

There is already a user contribution in the gromacs page named ffG43a1p, that is
based in the force field ffG43a1 and also includes phosphorilated serine end
threonine. However, is exciting doing it for yourself.
Mensaje citado por nahren manuel :

> Dear Gromacs Users,
>
> I am trying to simulate a protein whose Thr residues is phosphorylated.
> I did the following based on the earlier query regarding the same
> 
>  here is how I did it for phosphorylated Threonine.
>
>
> 1) open the appropriate .rtp file e.g. ffG43a1.rtp
> 2) make a copy of the existing entry for the residue
> you want to phosphorylate it.
>
> here are the notes I made as I did it...comments
> welcome if anyone
> doesnt like how I did it!
>
> ; TPO which follows is phosphorylated Threonine and
> was derived thus:
> ; 1) take THR entry
> ; 2) add P, O1P, O2P, O3P atoms
> ; 3) remove HG1 atom
> ; 4) assign partial charges to give an overall
> molecule -2 charge
> ; with this charge localised on the Phosphate
> group.
> ; 5) add bonds for OG1 to P and the OxPs. took bond
> tpyes from [ DADE ]
> ; 6) likewise took angle types from [ DADE ]
> ; 7) removed final dihedral which contained H1 (had
> considered changing
> it for
> ; P but dont want to limit Phoshphate group too
> much)
>
> 3) you will need to add the new residue to the file
> aminoacids.dat if
> you want the residue to be recognised as part of the
> protein in
> subsequent analysis. Make sure you increment the count
> on the top line
> of aminoacids.dat. dont put any comments in
> aminoacids.dat becuase it
> has unpredictable effects on results.
> 4) update the hydrogen database entry too if you are
> expecting pdb2gmx
> or protonate to work properly.
>
> I *think* that was it...!
> 
> Paul Barrett
>
> 
> but i get the following error
>  * * * * *
> Generated 380 of the 1326 non-bonded parameter combinations
> ERROR 0 [file "top_A.itp", line 16530]:
>   No default Proper Dih. types
> ERROR 0 [file "top_A.itp", line 16531]:
>   No default Proper Dih. types
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 3 bonded neighbours for Protein_B 1
> NOTE:
>   System has non-zero total charge: -1.96e+00
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   5789
> #  G96ANGLES:   8462
> #  PDIHS:   3040
> #  IDIHS:   2893
> #   LJ14:   9248
>
> ---
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1182
>
> Fatal error:
> There were 2 errors in input file(s)
> ---
>
> "Ich Bin Ein Berliner" (J.F. Kennedy)
> * * * * * *
>
> Kindly advice
> nahren
>
>
>
>
>
>


Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


Este mensaje fue enviado desde el servidor Webmail del Instituto de 
Biotecnologia.
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Re: [gmx-users] using more than one type of molecules

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Molecular Dynamics wrote:

Dear Justin,
 
I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the 
PRODRG. And you suggested that ' If these come from PRODRG, they will 
probably require manual modification and validation of their 
contents.' What kind of modifications should I do ? Could you please 
give me some 


1. If you are using the original PRODRG, don't.  The parameters it 
generates are for ffgmx, which is deprecated and should not be used.  
Use PRODRG-2.5 (beta server) and get a Gromos96 43a1-compatible topology.
2. The charges and charge groups assigned by PRODRG are inconsistent, at 
best. You will need to consult the manual for information about charge 
groups, and existing elements of the force field to determine whether or 
not the charges assigned are appropriate.




I should also add to this that just because you assign what you believe are 
reasonable parameters, does not mean they will necessarily be valid.  You must 
validate the parameters appropriately.  For Gromos96, this will involve 
measurements of thermodynamic variables and experimental observables.  Refer to 
the literature regarding the force field.  Parameterization is a time-consuming 
process.  While PRODRG does a nice job of automating topology construction, it 
is the task of the user to actually verify the applicability of the parameters.


-Justin

info about it ? And I 'm planning to obtain a binary mixture ( X : 120 
Y : 60 molecules number for example ) . According to your suggestions 
I will have used DRGGMX.ITP and DRGPOH.PDB  files of  X molecule, but 
I will just have used DRGGMX.ITP file of Y molecule. Isn't it 
important to use DRGPOH.PDB  file of Y molecule. Because Y is not a 
solvent. X and Y 


I'm not sure I fully understand.  You will obviously have to re-name the 
files to have them make any sense.  You also cannot call both of them 
"DRG" within the .pdb and .itp files, as is the output of PRODRG.


are organic molecules. And I think this is the unique way to obtain a 
binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could 
you explain these significant issues ?


Using genbox should be fine.

-Justin

 
Sincerely



*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Friday, March 13, 2009 8:25:14 PM
*Subject:* Re: [gmx-users] using more than one type of molecules



Molecular Dynamics wrote:
 >
 >
 > Dear All,
 >
 >
 > I'm new to Gromacs and have some questions to learn the answers. I 
study on one type molecule. If I want to add lets say 240 molecules, 
which is the best way to use editconf or genbox ? And I learned the 
procedure of using more than one type of molecules in gromacs. But I'm 
not sure, so I'm waiting for your contributions. Assume that I have 
two small organic


In general, the topol.top should consist of the #include statements 
for each .itp file, then the [ system ] directive should contain a 
count of each molecule.


Use editconf to set your box size, and genbox -ci -nmol to insert what 
you need.


 > molecules like hydrocarbons X and Y. I think First I will have to 
get seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in 
different


If these come from PRODRG, they will probably require manual 
modification and validation of their contents.


 > work directories. Then chose one directory ( X ) and do the 
operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then 
in this command

 >
 >
 > genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
 >
 >

If you are using X as the solute and Y as the solvent, then yes, this 
is fine. It is just like solvating a protein in water (if X = protein, 
Y = water).


 > After I get gmx.pdb gmx.top files I will add #include “Y.itp” and 
editing the number of Y molecule and go on ..

 >

Correct.

-Justin

 >
 > Could you please help me to learn the true process of using more 
than one type of molecules in gromacs ?

 >
 >
 >
 > Sincerely
 >
 >
 >
 > 


 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org 


 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!
 > Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to gmx-users-requ...@gromacs.org 
.

 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


_

Re: [gmx-users] using more than one type of molecules

[Justin A. Lemkul]

Molecular Dynamics wrote:

Dear Justin,
 
I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the 
PRODRG. And you suggested that ' If these come from PRODRG, they will 
probably require manual modification and validation of their contents.' 
What kind of modifications should I do ? Could you please give me some 


1. If you are using the original PRODRG, don't.  The parameters it generates are 
for ffgmx, which is deprecated and should not be used.  Use PRODRG-2.5 (beta 
server) and get a Gromos96 43a1-compatible topology.
2. The charges and charge groups assigned by PRODRG are inconsistent, at best. 
You will need to consult the manual for information about charge groups, and 
existing elements of the force field to determine whether or not the charges 
assigned are appropriate.


info about it ? And I 'm planning to obtain a binary mixture ( X : 120 Y 
: 60 molecules number for example ) . According to your suggestions I 
will have used DRGGMX.ITP and DRGPOH.PDB  files of  X molecule, but I 
will just have used DRGGMX.ITP file of Y molecule. Isn't it important to 
use DRGPOH.PDB  file of Y molecule. Because Y is not a solvent. X and Y 


I'm not sure I fully understand.  You will obviously have to re-name the files 
to have them make any sense.  You also cannot call both of them "DRG" within the 
.pdb and .itp files, as is the output of PRODRG.


are organic molecules. And I think this is the unique way to obtain a 
binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. Could 
you explain these significant issues ?


Using genbox should be fine.

-Justin

 
Sincerely



*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Friday, March 13, 2009 8:25:14 PM
*Subject:* Re: [gmx-users] using more than one type of molecules



Molecular Dynamics wrote:
 >
 >
 > Dear All,
 >
 >
 > I'm new to Gromacs and have some questions to learn the answers. I 
study on one type molecule. If I want to add lets say 240 molecules, 
which is the best way to use editconf or genbox ? And I learned the 
procedure of using more than one type of molecules in gromacs. But I'm 
not sure, so I'm waiting for your contributions. Assume that I have two 
small organic


In general, the topol.top should consist of the #include statements for 
each .itp file, then the [ system ] directive should contain a count of 
each molecule.


Use editconf to set your box size, and genbox -ci -nmol to insert what 
you need.


 > molecules like hydrocarbons X and Y. I think First I will have to get 
seperately DRGGMX.ITP and DRGPOH.PDB for the each molecules in different


If these come from PRODRG, they will probably require manual 
modification and validation of their contents.


 > work directories. Then chose one directory ( X ) and do the 
operations like in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then 
in this command

 >
 >
 > genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
 >
 >

If you are using X as the solute and Y as the solvent, then yes, this is 
fine. It is just like solvating a protein in water (if X = protein, Y = 
water).


 > After I get gmx.pdb gmx.top files I will add #include “Y.itp” and 
editing the number of Y molecule and go on ..

 >

Correct.

-Justin

 >
 > Could you please help me to learn the true process of using more than 
one type of molecules in gromacs ?

 >
 >
 >
 > Sincerely
 >
 >
 >
 > 
 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org 


 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!
 > Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to gmx-users-requ...@gromacs.org 
.

 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] how to parametrize Phos. Thr TPO

[Justin A. Lemkul]

nahren manuel wrote:





but i get the following error
 * * * * * 
Generated 380 of the 1326 non-bonded parameter combinations

ERROR 0 [file "top_A.itp", line 16530]:
  No default Proper Dih. types
ERROR 0
 [file "top_A.itp", line 16531]:
  No default Proper Dih. types


Then you haven't added all of the proper dihedrals for that particular molecule 
(phosphates are tricky).  There is a parameter set (ffG43a1p) that has a 
properly-derived set of parameters for phosphorylated amino acids in the User 
Contributions on the web site.


I recall that not all of the formatting was quite right in these files (they 
were designed for use with Gromacs 3.1.x, IIRC), so if you encounter errors you 
can contact me off-list and I can send you re-formatted files that I have gotten 
to work.


-Justin


Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
NOTE:
  System has non-zero total charge: -1.96e+00

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   5789
#  G96ANGLES:   8462
#  PDIHS:   3040
#  IDIHS:   2893
#   LJ14:   9248

---
Program grompp, VERSION 3.3.2
Source code file: grompp.c, line: 1182

Fatal error:
There were 2 errors in input file(s)
---

"Ich Bin Ein Berliner" (J.F. Kennedy)
* * * * * * 


Kindly advice
nahren






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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] ion jump out of protein

[Justin A. Lemkul]

Homa Azizian wrote:
Hi 
I mean after MD the ion was not in the active site, the location of ion is 
out of the protein.




Then your model physics is wrong and you will have to re-think/re-derive 
appropriate parameters.


-Justin

My ion jump out of the protein after MD.My ion (MN) has not any covalant 
bond by its neibour, just has electrostatic intraction. 
is there any line that I have to add to the itp file or top file in order 
to 
prevent this problem. 



--
Tehran University of Medical Sciences
www.tums.ac.ir




--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] using more than one type of molecules

[Molecular Dynamics]

Dear Justin,

I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And 
you suggested that ' If these come from PRODRG, they will probably require 
manual modification and validation of their contents.' What kind of 
modifications should I do ? Could you please give me some info about it ? And I 
'm planning to obtain a binary mixture ( X : 120 Y : 60 molecules number for 
example ) . According to your suggestions I will have used DRGGMX.ITP and 
DRGPOH.PDB  files of  X molecule, but I will just have used DRGGMX.ITP file of 
Y molecule. Isn't it important to use DRGPOH.PDB  file of Y molecule. Because Y 
is not a solvent. X and Y are organic molecules. And I think this is the unique 
way to obtain a binary mixture with using –cp X.pdb –cs Y.pdb in Gromacs usage. 
Could you explain these significant issues ? 

Sincerely





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Friday, March 13, 2009 8:25:14 PM
Subject: Re: [gmx-users] using more than one type of molecules



Molecular Dynamics wrote:
> 
> 
> Dear All,
> 
> 
> I'm new to Gromacs and have some questions to learn the answers. I study on 
> one type molecule. If I want to add lets say 240 molecules, which is the best 
> way to use editconf or genbox ? And I learned the procedure of using more 
> than one type of molecules in gromacs. But I'm not sure, so I'm waiting for 
> your contributions. Assume that I have two small organic 

In general, the topol.top should consist of the #include statements for each 
.itp file, then the [ system ] directive should contain a count of each 
molecule.

Use editconf to set your box size, and genbox -ci -nmol to insert what you need.

> molecules like hydrocarbons X and Y. I think First I will have to get 
> seperately DRGGMX.ITP and DRGPOH..PDB for the each molecules in different 

If these come from PRODRG, they will probably require manual modification and 
validation of their contents.

> work directories. Then chose one directory ( X ) and do the operations like 
> in ''GROMACS Tutorial for Drug – Enzyme Complex'' Then in this command
> 
> 
> genbox –cp X.pdb –cs Y.pdb –o gmx.pdb –p gmx.top
> 
> 

If you are using X as the solute and Y as the solvent, then yes, this is fine. 
It is just like solvating a protein in water (if X = protein, Y = water).

> After I get gmx.pdb gmx.top files I will add #include “Y.itp” and editing the 
> number of Y molecule and go on ..
> 

Correct.

-Justin

> 
> Could you please help me to learn the true process of using more than one 
> type of molecules in gromacs ?
> 
> 
> 
> Sincerely
> 
> 
> 
> 
> 
> ___
> gmx-users mailing list    gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] ion jump out of protein

[Homa Azizian]

Hi 
I mean after MD the ion was not in the active site, the location of ion is 
out of the protein.

> My ion jump out of the protein after MD.My ion (MN) has not any covalant 
> bond by its neibour, just has electrostatic intraction. 
> is there any line that I have to add to the itp file or top file in order 
> to 
> prevent this problem. 
> 

--
Tehran University of Medical Sciences
www.tums.ac.ir


-- 
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dangerous content by MailScanner, and is
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[gmx-users] how to parametrize Phos. Thr TPO

[nahren manuel]

Dear Gromacs Users,

I am trying to simulate a protein whose Thr residues is phosphorylated. 
I did the following based on the earlier query regarding the same

 here is how I did it for phosphorylated Threonine.


1) open the appropriate .rtp file e.g. ffG43a1.rtp
2) make a copy of the existing entry for the residue
you want to phosphorylate it.

here are the notes I made as I did it...comments
welcome if anyone
doesnt like how I did it!

; TPO which follows is phosphorylated Threonine and
was derived thus:
; 1) take THR entry
; 2) add P, O1P, O2P, O3P atoms
; 3) remove HG1 atom
; 4) assign partial charges to give an overall
molecule -2 charge
; with this charge localised on the Phosphate
group.
; 5) add bonds for OG1 to P and the OxPs. took bond
tpyes from [ DADE ]
; 6) likewise took angle types from [ DADE ]
; 7) removed final dihedral which contained H1 (had
considered changing
it for
; P but dont want to limit Phoshphate group too
much)

3) you will need to add the new residue to the file
aminoacids.dat if
you want the residue to be recognised as part of the
protein in
subsequent analysis. Make sure you increment the count
on the top line
of aminoacids.dat. dont put any comments in
aminoacids.dat becuase it
has unpredictable effects on results.
4) update the hydrogen database entry too if you are
expecting pdb2gmx
or protonate to work properly.

I *think* that was it...!

Paul Barrett


but i get the following error
 * * * * * 
Generated 380 of the 1326 non-bonded parameter combinations
ERROR 0 [file "top_A.itp", line 16530]:
  No default Proper Dih. types
ERROR 0 [file "top_A.itp", line 16531]:
  No default Proper Dih. types
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
NOTE:
  System has non-zero total charge: -1.96e+00

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   5789
#  G96ANGLES:   8462
#  PDIHS:   3040
#  IDIHS:   2893
#   LJ14:   9248

---
Program grompp, VERSION 3.3.2
Source code file: grompp.c, line: 1182

Fatal error:
There were 2 errors in input file(s)
---

"Ich Bin Ein Berliner" (J.F. Kennedy)
* * * * * * 

Kindly advice
nahren





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Re: [gmx-users] (no subject)

[Omer Markovitch]

Hello.
What do you mean by "jump"? Perhaps the "connected MN" is a stable state?
If you'll supply more details we could try to help you better.
--Omer.

On Sat, Mar 14, 2009 at 08:15, Homa Azizian wrote:

> My ion jump out of the protein after MD.My ion (MN) has not any covalant
> bond by its neibour, just has electrostatic intraction.
> is there any line that I have to add to the itp file or top file in order
> to
> prevent this problem.
>
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Re: [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

[David van der Spoel]

xiaowu...@hotmail.com wrote:
> Dear,
>   As a small test, I want to simulate polystyene(PS) using GROMACS. 
> Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating 
> unit(320 atoms totally ) and add the STY residues to the .rtp files. 
> while running pdb2gmx, the procedure was finished "successfully". but I 
> find that only 16 atoms are in the generated .gro and .top files. Have 
> you met this strange thing? Or tell me what I should do with it?
>  
The information you are sending here is not complete. How were termini
treated, hw was pdb2gmx invoked?
How do the building blocks in the rtp file and hdb file look like?

> Best regards,
> Chaofu Wu
> xiaowu...@hotmail.com 
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

[David van der Spoel]

Pietro Amodeo wrote:

ADDENDUM: I've just compiled Gromacs 3.3.3 on cluster NEW, with Intel
compiler (see below). A simulation (still running) on system 2 with the
paralled double-prec version shows preliminary results in line with
gromacs 3.3.1 on cluster OLD, with no trace of abnormal oscillations and
drifts in temperature or energy.


Please open a bugzilla and upload the different tpr files. If they 
indeed crash after short time it should be possible to see what is going on.



2) Cluster: NEW(Infiniband)

   (CentOS 5)
   kernel 2.6.18-53.el5
   icc 10.1 (Build 20070913 Pack.ID: l_cc_p_10.1.008)
   fftw 3.2.1
   ofed131 - openmpi 1.2.6


Best,
Pietro



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

[xiaowu759]

Dear,
  As a small test, I want to simulate polystyene(PS) using GROMACS. Firstly, I 
obtain a pdb file of a PS chain consisting of 20 repeating unit(320 atoms 
totally ) and add the STY residues to the .rtp files. while running pdb2gmx, 
the procedure was finished "successfully". but I find that only 16 atoms are in 
the generated .gro and .top files. Have you met this strange thing? Or tell me 
what I should do with it?

Best regards,
Chaofu Wu
xiaowu...@hotmail.com___
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Re: [gmx-users] Triclinic water box for a protein MD

[Tsjerk Wassenaar]

You're welcome. Forgot to mention that it comes with an additional
.mdp option (rototr = yes/no). That does break compatibility with
other versions regarding reading .tpr files.

Cheers,

Tsjerk

On Fri, Mar 13, 2009 at 10:48 PM, TJ Piggot  wrote:
> This looks great thanks, had meant to try and implement something like these
> restraints for ages but never got round to it, you know how it is ...
>
> Tom
>
> --On 13 March 2009 21:06 +0100 Tsjerk Wassenaar  wrote:
>
>> Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an
>> optimally packed system and simulate it with the Gromacs 3.3.1 version
>> you can download from
>> http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.3.1-rtc.tgz
>> That version of gromacs has the roto-translational constraints
>> implemented that were developed by Andrea Amadei.
>> Mind that the server is fresh :) The paper is about to be submitted.
>> Unfortunately I haven't had time to dig into the GMX 4 code to
>> implement the rotational constraints yet. I wouldn't want to
>> compromise the performance :S
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Mar 13, 2009 at 8:26 PM, TJ Piggot  wrote:
>>>
>>> You might want to try a rombic dodecahedron box (an option in editconf).
>>>
>>> Or you can run the simulation using a triclinic box hoping the images
>>> don't interact and then check after the simulation has finished using
>>> g_mindist -pi on the trajectory, bearing in mind if they do then you
>>> will have wasted a lot of time.
>>>
>>> If you do want to use a triclinic box having a larger amount of water
>>> surrounding the complex may be advisable as this makes images interacting
>>> less likely
>>>
>>> Tom
>>>
>>> --On Friday, March 13, 2009 20:10:05 +0100 Tsjerk Wassenaar
>>>  wrote:
>>>
 Hi,

 You have to make sure that you're molecule doesn't rotate. Otherwise
 it will cause direct interactions over the PBC. The same holds true
 for large conformational changes.

 Cheers,

 Tsjerk

 On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul 
 wrote:
>
>
> Lucio Montero wrote:
>>
>> I want to simulate a protein complex using a triclinic box, because it
>> reduce my system size in 60%, and consequently the computing time. I
>> have read that using a triclinic box can give problems for a long MD
>> if the peptide has a whirl, but I don´t know if it is a problem for a
>> complex of ~ 530 aa (protein 1: 376 aa, protein 2: 132 aa, protein 3:
>> 20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of
>> water. I want to run the MD simulating 20 ns.
>
> What problems have you read about?  Can you cite a source so we know
> what you're talking about?
>
> -Justin
>
>> Best regards,
>> Lucio Montero
>>
>>  
>> -- -- Lucio
>> Ricardo Montero Valenzuela
>> Laboratorio del Dr. Federico Sánchez
>> Ext. 27666
>> Departamento de Biología Molecular de Plantas
>> Instituto de Biotecnología, UNAM
>> Cuernavaca, Morelos, 62210
>>
>>
>> -
>> ---
>>
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>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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 --
 Tsjerk A. Wassenaar, Ph.D.
 Junior UD (post-doc)
 Biomolecular NMR, Bijvoet Center
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 P: +31-30-2539931
 F: +31-30-2537623
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