[gmx-users] Topology generation of molecules

Smith, Micholas D. smithmd at ornl.gov
Tue Jun 20 14:08:21 CEST 2017


Channa,

What are you trying to use the Topology for? MD or Analysis of a trajectory from some other piece of software? Justin is right, if you want to run MD than you can't just use one force-field server to generate another, as each one has will give output for different force-fields and each force-field may (read: will) lead to different dynamics. However: If you are just trying to analyze a trajectory your built with some other software (like NAMD), you can use topotools ( https://sites.google.com/site/akohlmey/software/topotools ) to convert a psf into a gromacs topology with "non-sense" force-field parameters but the correct bond, dihedrial and angle portion of the topology file, which will let you use grompp to make a *.tpr for the analysis tools.

-Micholas

===================
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 Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, June 20, 2017 7:58 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Topology generation of molecules

On 6/20/17 12:21 AM, Abid Channa wrote:
> If PRODRG is not giving suitable results . Can I use Antechamber output in GROMACS for the topology generation of molecules ?  .

PRODRG is for GROMOS, Antechamber is for AMBER.  You can't simply replace one
with the other because the force fields are totally different.  Parametrize your
molecule in a manner consistent with the parent biomolecular force field, or
find the program/server that is consistent with that force field.

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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