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

[Justin Lemkul]

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
20 Penn St.
Baltimore, MD 21201

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

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