[gmx-users] pdb (CTAB) into .GRO
Smith, Micholas D.
smithmd at ornl.gov
Fri Nov 3 15:38:34 CET 2017
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.
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
> 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?
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