[gmx-users] itp file problem

[Justin A. Lemkul]

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

-- 
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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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