[gmx-users] oplsaa parametrization

Ran Friedman r.friedman at bioc.uzh.ch
Mon May 25 12:16:03 CEST 2009

R. A. wrote:
> Dear Users
> I m trying to simulate a structure (not a protein) which is not
> parametrized in oplsaa FF. I created the structure using PRODRG and
> included the results of *.itp from PRODRG to ffoplsaa.rtp file and
> tried to use available oplss_xxx for my atom type near to those ones
> already exists in *.atp. I also optimized my structure at RHF/6-31G*
> level and calculated the charge using resp. Then updated ffoplsaa.rtp
> using this calculated charge. By refering to the mailing list it seems
> that I need to modify bn.itp and nob.itp file as well (?!). I m just
> wonder if anybody use PRODRG how he/she parametrized FF. As I m new in
> GROMACS and any tutorial or procedure to follow will help me so much.
> Thank you in advance for any ideas or comments.
As far as I know PRODRG doesn't produce itp files comparable with OPLS,
so you need to use something else or manual modifications.


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