[gmx-users] How can I create the OPLS-AA topology file for the liagnd

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 12 09:23:12 CEST 2009

Ms. Aswathy S wrote:
> Hi,
> i would like to do a ligand -receptor simulation using OPLS-AA force field. I suppose using the options in Gromacs I can create the itp files for protein only. But how can i create the OPLS --AA topology file for the ligand. I think PRODRG server only creates gromacs force field. Please coreect me if my understanding is wrong.

You have to create one by hand. You might use one from PRODRG as a 
formatting template. You might work from elements of existing amino 
acids. Depending on the ligand you might have a 
http://oldwiki.gromacs.org/index.php/Parameterization problem.


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