[gmx-users] Full topology from pdf2gmx

Justin Lemkul jalemkul at vt.edu
Thu Aug 4 00:13:50 CEST 2016

On 8/3/16 11:18 AM, Eric Smoll wrote:
> Hello GROMACS users,
> Pdb2gmx generates a topology without parameters under directives like
> bonds, angles, etc. This is because it references information in the
> specified forcefield database. Is it possible to generate a fully populated
> topology with force constants, equilibrium distances, etc.?

Try grompp -pp.



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


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