[gmx-users] develop parameters for small molecules

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 31 11:35:36 CET 2012

On 2012-01-31 11:28, Qinghua Liao wrote:
> Dear GMX users,
> We want to develop the ff parameters for some small molecules in
> consistent with gromos 53a6, and I know that PRODRG can do it, but it is
> not accurate enough. So we want to do some QM calculations to validate
> it. However, how can I derive these parameters for bonds and dihedrals
> from QM calculations, and also the partial charge. In Amber, antechamber
> can do it, so is there also such a tool for gromacs? Any suggestion will
> be appreciated.
> --
> Best Regards,
> Qinghua
Before you do it yourself:

Check http://compbio.biosci.uq.edu.au/atb/ for gromos parameters
or http://virtualchemistry.org/ for OPLS/AA and GAFF alternatively
http://mackerell.umaryland.edu/~kenno/cgenff for the Charmm generalized FF.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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