[gmx-users] grompp

[Justin Lemkul]

On 6/18/14, 8:20 AM, Meenakshi Rajput wrote:
> Hi I have made my ligand coordinate file using prodrg server. And the 15
> missing atoms are the ligand atoms as they are not seen in gro file. I have
> modified protein's topology file. Is there any change i have to make in gro
> file except adding ligand coordinates?
>

Follow this protocol:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

You'll undoubtedly need to correct the PRODRG topology (I probably say that at 
least once a week).

-Justin

-- 
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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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