[gmx-users] optimizing GAFF2 torsional parameters

Scott Brozell srb at osc.edu
Wed Sep 11 19:22:47 CEST 2019


I do not have answers to your questions.  Just in case you do not
know, Junmei Wang and David Case (GAFF developers) follow the Amber
reflector: AMBER Mailing List <amber at ambermd.org>
See ambermd.org for subscription info.


On Mon, Sep 09, 2019 at 09:31:21AM -0500, Christos Deligkaris wrote:
> I am trying to improve the GAFF2 dihedral parameters for a torsion on a
> small molecule. My small molecule has 5 torsions, only one is problematic,
> I have been able to improve the dihedral parameters for the other 4
> torsions by adjusting the force constants of the GAFF2 dihedral terms.
> In the figure shown here (PDF file):
> https://drive.google.com/file/d/1IkqoZ2CPEexZlAYt_DuQMqHzjGKWE6zK/view?usp=sharing
> red is QM, green is GAFF2, blue is one of my attempts to improve the
> results. The somewhat improved energy maximum at 0 degrees comes with an
> artificial minimum at around -30 degrees. This minimum seems to also be
> present at the default GAFF2 torsional profile but it is more shallow.
> I can increase the weights of the points around the artificial minimum to
> make them more consistent with QM data, but of course that comes at the
> expense of less agreement with QM data at around -180- -120 degrees. I have
> also tried optimizing the phase angles, without restricting them to 0 or
> 180, but that introduces an additional artificial energy minimum at around
> -150 degrees. I have also tried all possible multiplicities, 1,2,3 without
> any luck. I am using Mathematica to do the optimization.
> What strategies have people used in the past to improve agreement of
> dihedral parameters with QM data? Are there reasons to prefer no artificial
> energy minima versus better agreement on energy barriers?
> Best wishes,
> Christos Deligkaris, PhD
> Assistant Professor of Physics, University of Southern Indiana
> SC2220, 8600 University Blvd, Evansville IN, 47712
> Office Phone: (812) 228-5056
> www.deligkaris.org @DeligkarisGroup

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