[gmx-users] How can I create the OPLS-AA topology file for the liagnd
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 12 09:27:37 CEST 2009
Mark Abraham wrote:
> Ms. Aswathy S wrote:
>> 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.
Do also check the user contributions, e.g. topolbuild or mktop that can
be downloaded from the old website.
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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