[gmx-users] Topology error

[Abid Channa]

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 ,,,,,
Thanks,,
Regards,,

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