[gmx-users] pdb2gmx -chainsep vs -merge

[nahren manuel]

Dear Gromacs Users,

Tsjerk, 

the original file did not contain OXT, as you can see, it has O1 &
O2, so I removed the O2 from the PDB and renamed O1 to OXT.

ATOM   2841  HG  CYS R 283     -24.270  89.566  -4.957  1.00  0.00           H
ATOM   2842  C   CYS R 283     -25.867  92.922  -7.562  1.00  0.00           C
ATOM   2843  O1  CYS R 283     -26.993  93.593  -7.927  1.00  0.00           O
ATOM   2844  O2  CYS R 283     -24.611  93.156  -8.027  1.00  0.00           O
ATOM   2845  N   LYS B 284     -23.431 108.789  63.478  1.00  0.00           N
ATOM   2846  H1  LYS B 284     -23.779 109.339  64.238  1.00  0.00           H



sed -i '/^ATOM.*O2/d' DIMER.pdb

Am i going wrong here....?

the original PDB file is here : 

http://www.4shared.com/account/file/bTulGDPs/DIMER_FINAL.html

Best,
nahren

--- On Tue, 9/7/10, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, September 7, 2010, 12:22 PM

Hi Nahren,

Can you paste your actual command line where you used sed?

Cheers,

Tsjerk

On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel <meetnahren at yahoo.com> wrote:


Dear Gromacs Users,

thanks for all your suggestions. 

Tsjerk, I did try your idea, but unfortunately doesn't seem to work.

the pdb file is shared here : http://www.4shared.com/account/file/ijofD83b/DIMER.html


newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh 

Fatal error:
Atom OXT in residue CYS 283 was not found in rtp entry CYS with 11 atoms
while sorting atoms.
.


Part of the file is pasted below:


ATOM   2836  N   CYS R 283     -27.431  91.636  -6.099  1.00  0.00           N
ATOM   2837  H   CYS R 283     -27.855  90.779  -6.392  1.00  0.00          
 H
ATOM   2838  CA  CYS R 283     -26.033  91.780  -6.514  1.00  0.00           C
ATOM   2839  CB  CYS R 283     -25.500  90.433  -7.060  1.00  0.00           C
ATOM   2840  SG  CYS R 283     -25.121  89.114  -5.829  1.00  0.00           S

ATOM   2841  HG  CYS R 283     -24.270  89.566  -4.957  1.00  0.00           H
ATOM   2842  C   CYS R 283     -25.867  92.922  -7.562  1.00  0.00          
 C
ATOM   2843  OXT CYS R 283     -26.993  93.593  -7.927  1.00  0.00           O
ATOM   2845  N   LYS B 284     -23.431 108.789  63.478  1.00  0.00           N
ATOM   2846  H1  LYS B 284     -23.779 109.339  64.238  1.00  0.00           H

ATOM   2847  H2  LYS B 284     -23.156 109.392  62.730  1.00  0.00           H


Best,
nahren

--- On Tue, 9/7/10, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:


From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge

To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, September 7, 2010, 11:14 AM


Hi,

> One work-around for the -chainsep situation you've observed is to remove or rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when it tries to merge the chains. It should be taking care of that itself, but handling it yourself might help. pdb2gmx can probably rebuild the carboxyl oxygen. Keeping (one of the) OXT atoms and renaming it to "O" (keeping the fixed-column format correct) might be needed.


There should be only one OXT per chain. Removing those seems like a good idea:

sed -i '/^ATOM.*OXT/d' file.pdb
(Remove all lines starting with ATOM and containing OXT, in the file)

Hope it helps,


Tsjerk


--
Tsjerk A.
 Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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-- 
Tsjerk A. Wassenaar, Ph.D.


post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology / 
University of Groningen
The Netherlands


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