[gmx-users] itp file

[Lovika Moudgil]

Thanks Justin ... I will try as you said!!


Regards
Lovika

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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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