[gmx-users] Topology error

Abid Channa abid_channa04 at yahoo.com
Tue Apr 7 14:23:31 CEST 2015

Dear gromacs users,
I am working on protein-ligand simulation, I have prepared ligand topology through PRODRG server, it is generating many files , I am taking co-ordinate file Gromos-87/Gromacs (polar/aromatic hydrogens) and gromacs topoplogy file interms "drg.itp", problem is that PRODRG only take unprotonated form while I am giving input file with protonated form , prodrg delete all the hydrogens, my ligand has 58 atoms , while PRODRG only generate 36 atoms topoly and coordinate file, PRODRG also generate all hydrogen file when I take that file topolgy error occurs in topol.top file and solv.gro file,, waiting for comments from all of you specially from Justin ,,,,,

Abid Ali Channa,Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,Dr .Panjwani Center for Molecular Medicine and Drug Research,International Center for Chemical and Biological Sciences,University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309)Cell # +923013553051

More information about the gromacs.org_gmx-users mailing list