On 5/16/12 2:25 PM, Sarath Kumar Baskaran wrote:
Hi,
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
The newer version of the PRODRG server is compatible with Gromos96 43a1, not the
old "ffgmx," which was a variant of Gromos87. Using 43a1 should solve the problem.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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