[gmx-users] Assigning charges to Proline residues
jalemkul at vt.edu
Tue Aug 30 17:31:15 CEST 2016
On 8/30/16 11:28 AM, Dan Woodall wrote:
> I'm looking to define the charges on a 10 residue polypeptide using
> pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
> charged, but I can only find ways to assign charges to the amino acids that
> typically carry charges. Is there a way I can force the program to
> recognize a +1 charge (protonated) on a proline?
You need to define a new residue entry in the .rtp file for this specific
proline type, then assign that new residue name to the residue in the coordinate
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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