[gmx-users] Modified peptides

sun sun.iba2 at gmail.com
Tue Feb 2 17:02:36 CET 2016

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?  


Sent from my iPhone

More information about the gromacs.org_gmx-users mailing list