[gmx-users] Atomistic Simulation

Justin Lemkul jalemkul at vt.edu
Wed Dec 4 15:17:44 CET 2013

On 12/4/13 9:06 AM, panzu wrote:
> so How do I convert from .pdb to .gro the ?

You don't technically need one:


If you prefer to use .gro format, just convert with editconf.  The job of 
pdb2gmx is to produce a topology; the output of a force field-compliant 
structure is a side effect.  You already have a matching structure and a 
topology, so there's no need to run pdb2gmx.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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