[gmx-users] Modified peptides

Justin Lemkul jalemkul at vt.edu
Wed Feb 3 12:07:51 CET 2016

On 2/2/16 11:02 AM, sun wrote:
> Hello
> I want to do protein-ligand MD with Gromos-43A1 ff. My ligand is a tripeptide with a heterocyclic ring  attached to -N terminus. I read in Justin's tutorial, for non-peptidic ligands, one can obtain co-ordinates from PRODRG server. My question is, if i can obtain the co-ordinates for modified peptide as well? Will it behave like a peptide then? Or should i define the paramenters for ring,alone, from PRODRG, run pdb2gmx for peptide lligand and then combine the co-ordinates into a file and then prepare topology for my protein and make complex.gro?

You should not use PRODRG for anything; its parameters are quite unreliable.

Use the protein force field for anything with protein and develop parameters for 
the rest.  This will involve parametrizing a suitable model compound that 
contains the linkage to the peptide, so that the topology can be merged easily 
to create a new residue or terminus definition.



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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