[gmx-users] Topology generation of molecules

[Justin Lemkul]

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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