[gmx-users] Topology generation of molecules

[Smith, Micholas D.]

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
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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