[gmx-users] itp file
lovikamoudgil at gmail.com
Fri Sep 12 06:03:20 CEST 2014
Thanks Justin ... I will try as you said!!
On Thu, Sep 11, 2014 at 6:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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