[gmx-users] how to treat the peptide apart from the ligand -reg

[Justin Lemkul]

On 10/19/14 12:36 PM, venkatesh s wrote:
> i generated peptide  .gro .file and top using *prodrg *server
>
> so here after how to update the topol.top ? (Distance restrain or potions
> restrain ? )
>

You shouldn't use PRODRG for peptide ligands; the parameters are totally 
inconsistent with the parent force field.  You need to find a force field that 
supports phosphoproteins.  There are some available on 
http://www.gromacs.org/Downloads/User_contributions/Force_fields

-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 629
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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