[gmx-users] pdb (CTAB) into .GRO

[Smith, Micholas D.]

One thing to try is to build the CTAB molecule with gmx x2top. You'll need to be careful about what it produces, but it can be helpful.


===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Tasneem Kausar <tasneemkausar12 at gmail.com>
Sent: Friday, November 03, 2017 6:35 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pdb (CTAB) into .GRO

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In
your pdb file residue name XXX is not defined in gromos ff. If your system
is other than protein then use ATB to generate topolgy.

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On Fri, Nov 3, 2017 at 2:19 PM, Adriano Santana Sanchez <
adriano.santanasanchez at kaust.edu.sa> wrote:

>  Dear all,
>
>  I am a beginner with gromacs and I have already done some online
> tutorials.
>  I am now trying to create from a PDB coordinate file (a CTAB molecule) the
>  corresponding .GRO and .TOP files to run MD simulations.
>
>  gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
>
>  then choose FF gromos96 53a6 but get error message:
>
>  Residue 'XXX' not found in topology database
>
> I am sure this FF has been used for this molecule before and I cannot
>
> find this CTAB on the residue database. What can I do?
>
> Thanks,
> Adriano
>
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