On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote:
Hi all!
Context
I'm trying to run simple gromacs example commands below
* gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce
* gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
-water spc
In a Do
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 "
On 3/17/20 1:00 PM, Max Winokan wrote:
Dear GMX-Users,
Firstly, in light of the current situation with CoVID-19 I would like to wish
everyone the best of luck with staying healthy and safe during these uncertain
times. Now on to my Gromacs issue:
I am relatively new to Gromacs and
On 2/7/20 8:38 AM, i.i...@bioc.uzh.ch wrote:
Dear gmx users,
I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated
cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs
does no
On 1/17/20 4:25 AM, András Ferenc WACHA wrote:
Dear Justin,
there are no name clashes in the .rtp files by design, I never re-use
already existing residue names. Beta3-homo-lysine is B3K,
beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
naming scheme.
Sorry, no idea. T
Dear Justin,
there are no name clashes in the .rtp files by design, I never re-use
already existing residue names. Beta3-homo-lysine is B3K,
beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
naming scheme.
Andras
On 1/16/20 11:34 PM, Justin Lemkul wrote:
>
>
> On 1/16/20 10
On 1/16/20 10:07 AM, András Ferenc WACHA wrote:
Dear Justin,
thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and ma
Dear Justin,
thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and maintainability)?
Kind regards,
Andras
On 1/16/20 2:47
On 1/16/20 8:44 AM, András Ferenc WACHA wrote:
Sorry, now replying to the whole list:
Dear Justin,
I have obtained the base force field from the website of the MacKerell
Lab
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
I have checked a
Sorry, now replying to the whole list:
Dear Justin,
I have obtained the base force field from the website of the MacKerell
Lab
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz).
I have checked and the merged.n.tdb file is the same in my version
On 1/16/20 8:04 AM, András Ferenc WACHA wrote:
Dear fellow Gromacs users,
I have developed an extended version of the CHARMM36m force field for
beta-amino acids (https://charmm-betaff.readthedocs.io,
https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found
pdb2gmx works well. Ho
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
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 c
Hi,
Leave the rtp the way it was and name the residue in the pdb file so that
it matches. Then you won't have to teach pdb2gmx that your newly invented
residue is protein
Mark
On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, <
neena.susaneap...@mail.utoronto.ca> wrote:
> Hi GMX users,
>
>
> 1
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
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 "s
mx-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 GROMOS53a6CARBO. The atom
> names were modified according to the rtp file of the force field. Yet,
> I get t
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 n
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 - Pr
ion:
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:
prin
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:
> H
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
Hi again,
It seems from previous posts that this type of system setup is of general
interest so I thought I'd share the solution(s).
I modified the tdb file for the 5' end, here for CHARMM27, by adding the
following to the end of dna.n.tdb
[ hack ]
[ replace ]
C5' C5' CN8B12.011
Thanks, but it doesn't work. Same problem.
Gianmarco Bartalini
Il 27 nov 2017 14:37, "Justin Lemkul" ha scritto:
>
>
> On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
>
>> Hello guys, I produced a system "protein + lipid membrane" using the
>> online
>> tool CHARMM-GUI. Since I need to use the
On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
Hello guys, I produced a system "protein + lipid membrane" using the online
tool CHARMM-GUI. Since I need to use the Amber force field, I added the
Lipids17 force field inside Gromacs. The implementation should work fine,
since the conversion of a
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
Dear Mark Abraham,
Thank you so much for debugging it for me. The strange word could only be seen
under Unix environment. After using dos2unix, the problem finally solves!
I totally forgot to always use dos2unix. Thanks a lot for reminding me again!
Yours sincerely
Cheng
-
Hi,
Some of your PDB files are malformed, which you could see with the less
tool, or probably anything else. The first line, containing N, leads with
strange characters, which stops pdb2gmx recognizing that they start with
"ATOM," since they don't. Then N are recognized as missing.
Mark
On Sat,
Dear Justin,
The command line that got fatal error is:
gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh
-merge interactive
The command line that works fine is:
gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge
interactive
(just change
On 5/19/17 6:31 PM, ZHANG Cheng wrote:
Dear Justin,
I replied the thread already, but it is waiting for approval due to large email
content. Could you please approve it?
I have no control over that. If it's too much for an email (normally pdb2gmx
output is fine) then upload to e.g. pasteb
Dear Justin,
I replied the thread already, but it is waiting for approval due to large email
content. Could you please approve it?
Cheng
---Original---
From: "ZHANG Cheng"<272699...@qq.com>
Date: 2017/5/19 22:37:52
To: "gromacs.org_gmx-users";
Cc: "QQ"<272699...@qq.com>;
Subject: pdb2gmx: At
On 5/19/17 5:37 PM, ZHANG Cheng wrote:
Dear Gromacs,
I got this fatal error after running "pdb2gmx":
Please provide your exact command and full screen output. There's a lot of
relevant information there, because pdb2gmx is doing a lot of complex things.
-Justin
Fatal error:
Residue 1
On 5/10/17 4:16 AM, Changdong LIU wrote:
Dear GROMACS users,
I used pdb2gmx to generate topology file for the g_quadruplex DNA which
constains 3 potassiums.
If the 3 potassiums were deleted ,the pdb2gma successfully generated the
topology file for DNA.
But failed when the 3 potassiums
Take a look at you pdb file. May be potassium atom is defined as HETATM in
pdb. amber99sb-ildn ff has K in its ions.itp file.
On Wed, May 10, 2017 at 1:46 PM, Changdong LIU wrote:
> Dear GROMACS users,
>
>
> I used pdb2gmx to generate topology file for the g_quadruplex DNA which
> constains 3 p
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-in
So I found out why I didn't use charmm-gui initially, when using the
protein membrane builder it removes the ligand minocycline. I have found a
solution, on the unlikely chance what I have done will help someone, I'm
going to post what I did.
Since I used transformations on the protein (aligning t
On 3/13/17 1:48 PM, Davit Hakobyan wrote:
Just a small note about cholesterol CHL1 in the merged.rtp file of november 2016
release for CHARMM36 force field.
The first four lines of CHL1 in merged.rtp:
C3 CRL10.140 0
O3 OHL -0.660 1
H3' HOL0.430 2
H3
I honestly forgot why (took too long, erred, or both) so I tried to do
charm-gui again. From my current attempt it is taking a while. I'm on the
last step and I'll keep checking the output.
I'll keep you updated when something happens.
Thanks again, your help is invaluable!
- Jonathan
P.S. I am
Just a small note about cholesterol CHL1 in the merged.rtp file of
november 2016 release for CHARMM36 force field.
The first four lines of CHL1 in merged.rtp:
C3 CRL10.140 0
O3 OHL -0.660 1
H3' HOL0.430 2
H3 HGA10.090 3
While the sequence should
Thank you very much!
Indeed, it seems the problem was in the missing TER lines in combination
with -chainsep for individual chain separation.
Thank you again for all your kind help.
Davit
On 3/13/2017 6:21 PM, Justin Lemkul wrote:
On 3/13/17 1:12 PM, Davit Hakobyan wrote:
Thank you for th
Thank you.
I have put the ZIP of the PDB file here:
https://uni-muenster.sciebo.de/index.php/s/hO1OwfWMwwOy7xe
The encountered error with the ASP residue relates to the C-terminal
patch of the ANAA molecule which pdb2gmx missed and treating it as an
unpatched ASP would give, of course, a misma
On 3/13/17 1:12 PM, Davit Hakobyan wrote:
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 i
Hi,
Using -ter to specify where molecules end won't help if there are not any
TER records, but I can't tell what's in your file :-)
Mark
On Mon, Mar 13, 2017 at 6:12 PM Davit Hakobyan
wrote:
> Thank you for the suggestion.
>
> I have tried to use the "-ter" flagbut this does not helpsince the
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
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
On 3/12/17 8:36 PM, Jonathan Saboury wrote:
Hello all,
I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization,
equilibration, and production runs given. Then I copied the 10ns production
run .gro to a different folder so that I can run it with
charmm36-nov2016.ff instead of
Thank you so much! It worked! Really appreciate the quick reply.
Acqualine Lobo
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On 3/2/17 9:18 AM, Acqualine Lobo wrote:
Thanks for the quick reply Dr. Justin!
I did follow what you mentioned, however I still get the same error. I also
tried changing the residue name in the pdb file to match the atom type as
in the .atp file, the error still remains only with a different
Thanks for the quick reply Dr. Justin!
I did follow what you mentioned, however I still get the same error. I also
tried changing the residue name in the pdb file to match the atom type as
in the .atp file, the error still remains only with a different residue
name. Instead of "Residue 'CMO' not f
On 3/1/17 7:29 AM, Acqualine Lobo wrote:
Hello,
I am trying to simulate a hemoglobin molecule in complex with CO. However,
pdb2gmx throws a fatal error saying
Fatal error:
Residue 'CMO' not found in residue topology database
For more information and tips for troubleshooting, please check the
>>> 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 cal
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
>
> 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 pr
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
>
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 > a
-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
t 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: gm
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 y
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
--
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.n
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 construc
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, Just
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
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 ent
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 hep
Thank you Justin!!! That's the problem. Now everything runs well.
Ruan
On Tue, May 3, 2016 at 12:04 PM, Justin Lemkul wrote:
>
>
> On 5/3/16 12:02 PM, Zheng Ruan wrote:
>
>> Hi Gromacs Users,
>>
>> I'm using pdb2gmx to process my pdb files with a phospho-tyrosine
>> using amber99sb-ildn.ff. The
On 5/3/16 12:02 PM, Zheng Ruan wrote:
Hi Gromacs Users,
I'm using pdb2gmx to process my pdb files with a phospho-tyrosine
using amber99sb-ildn.ff. The relavant content in my pdb looks like this
(There is a serine before phosphorylated tyrosine):
ATOM202 N SER26 31.593 -68.669
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
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,
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
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:
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 happe
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 (-:
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:
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,
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
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
On 2/23/16 10:31 PM, Ray Chao wrote:
Hi, gmx users,
I used materials studio to generate a .pdb file containing 160 PTFE chains,
and then modified the oplsaa forcefiled as Justin did. The pdb2gmx
generated right .gro and .top files. But the problem is that it generated
one .itp file for each
Hi ,
Maybe you can try -merge all when using pdb2gmx.
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htt
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 structu
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 #defi
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 fr
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 t
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. Imr
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=O
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 s
Maxim Igaev писал 13-01-2016 19:51:
Dear Gromacs users,
I have a large molecular complex consisting of many identical monomers.
I constructed a pdb file for it using VMD and assigned each monomer
a segment name (A0, A1, A2 etc.). The chain name was however always
the same - A. Then I created the
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 w
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...@gm
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
Hi,
Unfortunately, pdb2gmx is only aware of chain ids, so you will not be able
to preserve segment id. If the atom ordering is unchanged then you don't
need the resulting PDB file, ie can use the original one. If not, then it's
straightforward to use some scripting tool to re-unite your segment id
I have had this problem and I suspect that the answer lies in the Fatal error
you receive. Grimace will not allow you to have dangling bonds. Something has
to be attached to the first and last bond, otherwise it is not a viable
molecule.
Peter
Sent from my iPad
> On 2 בדצמ׳ 2015, at 18:03,
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 any
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
construc
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
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
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
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
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,
>>
>> Thi
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-termina
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