[gmx-users] pdb2gmx -chainsep vs -merge

[Tsjerk Wassenaar]

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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