[gmx-users] protein topology

Justin Lemkul jalemkul at vt.edu
Tue Oct 27 14:02:45 CET 2015

On 10/27/15 8:44 AM, Nikhil wrote:
> Thanks for your replay
> here is the problem
> my initial protein contain 8300 atoms with hydrogen,i deleted hydrogen
> then it comes around 4100 atoms,after pdb2gmx it become 5300 but doubt is
> what about remaining 3000 atoms? or hydrogens?
> if i take with the 5300 atoms and follow the simulation it will be fine?
> or is there anything im missing out here?

You should read a bit about united-atom force fields, and 43a1 specifically, 
before using it for a simulation.  Understanding the force field should be 
prerequisite before ever trying to do a simulation with one.



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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