[gmx-users] itp file problem

Sarath Kumar Baskaran bskumar.tech at gmail.com
Wed May 16 20:25:49 CEST 2012

For the simulation of a Protein ligand complex, i obtained the itp topology
of the ligand from PRODRG 2 server and i ran the simulation of the complex
a year back using GROMOS united atom force field by -ff gmx option in
GROMACS 3.3 according to the Drg enzyme tutorial
now i am unable to run the same protein ligand complex with the recent itp
file obtained from the Current PRODRG server for the same ligand, i am
getting error ATOM type CR1 not found in GROMACS 4.0.5. I am sure version
of gromacs doesnt create any problem.
Also i am getting atom mismatch error if i change the ATOM type to CR61,
and i completely checked this number of atoms mismatch is only due to the
.itp file included in prt.top.
Thanks to justin for saying me about the problems in PRODRG topology, and
suggesting to do improvements in the topology file for GROMOS force field,
But i am totally confused how to edit the itp file. Before i used to
include .itp file in .top file and add the residue number as DRG 1. now how
to edit the .itp file, Somebody please help me

**Keep Enjoying !!!*

*Yours Sincerely,*
*B. Sarath Kumar, M.S (By Research),
Tissue Culture and Drug Discovery Lab,
Centre for Biotechnology,
Anna University, Chennai.*
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