[gmx-users] Regarding error while generating topology for protein

Justin Lemkul jalemkul at vt.edu
Mon Mar 7 15:01:31 CET 2016



On 3/7/16 6:31 AM, shrikant kaushik wrote:
> hello sir,
>    I have query related to topology file generation for my protein, THR
> residue is Phosphorylated  (TPO), it showing error while running pdbtogmx.
> how to generate topology file for protein along with TPO residue.
>

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Many force fields support phosphorylated residues, you need to use one that does.

-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
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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