[gmx-users] itp file

Justin Lemkul jalemkul at vt.edu
Thu Sep 11 14:38:18 CEST 2014

On 9/11/14 6:09 AM, Lovika Moudgil wrote:
> Thanks for reply Lalit , Actually  my system have citrate anion and I want
> .itp for citrate and further I will use OPLA/SS force field!! It can't be
> generated be pdb2gmx!!

The OPLS-AA strategy is generally similar to GROMOS - you can piece the molecule 
together from existing functional groups.  Since the force field already covers 
everything you need for citrate, assigning charges and atomtypes is 
straightforward.  You can create an .rtp entry for it and have pdb2gmx do all 
the work of assigning the bonded interactions (you need to specify the [bonds], 
pdb2gmx does the rest).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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