[gmx-users] GROMACS compatible Charmm36 Phospho residues
jalemkul at vt.edu
Wed Oct 21 23:34:09 CEST 2015
On 10/21/15 5:31 PM, Parker de Waal wrote:
> Hi Everyone,
> I'd like to use the phosphoserine/threonine parameters from http://mackerell.umaryland.edu/charmm_ff.shtml, however it isn't obvious how to apply these without manually editing the charmm36 forcefield files.
> Does anyone know the proper way incorporate these paramters/have already done this and would be willing to share?
All phosphorylated residues are already present and ready for use. You just
need to add them to residuetypes.dat before running pdb2gmx.
; monoanionic phosphoserine
[ SP1 ]
; dianionic phosphoserine
[ SP2 ]
; monoanionic phosphothreonine
[ THP1 ]
; dianionic phosphothreonine
[ THP2 ]
; monoanionic phosphotyrosine
[ TP1 ]
; dianionic phosphotyrosine
[ TP2 ]
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
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