ff19SB will not be related to the behavior of the small molecule, that
comes from the small molecule force field. You do not say how you obtained
those parameters. You mention Gaussian but that is probably for the
partial atomic charges. What small molecule force field did you use -
perhaps GAFF or GAFF2?
also, the rings will not always be planar, they likely fluctuate and you
will see non-planar snapshots. On average it should be planar. Are you
seeing a specific problem? maybe you could measure a ring dihedral angle
and see if the average is 0 radians.
On Mon, Apr 1, 2024 at 3:28 PM Intravaia, Lauren E via AMBER <
amber.ambermd.org> wrote:
> Hello,
>
> I am performing MD simulations of enzyme-inhibitor complexes using AMBER
> ff19sb forcefield. I noticed that benzene rings on the small molecular do
> not remain planar throughout the simulation. I derived forcefield
> parameters after geometry optimization and ESP calculation with gaussian.
> Is there anything I can do to maintain planarity of the planar rings during
> the simulation?
>
> Thank you,
> Lauren
>
> --
> Lauren Intravaia
> PhD Candidate
> Lab of Dr. Celia Schiffer
> Dept. of Biochemistry and Molecular Biotechnology
> University of Massachusetts Chan Medical School
> 364 Plantation St. LRB 970D
> Email: lauren.intravaia.umassmed.edu<mailto:lauren.intravaia.umassmed.edu>
> Website: https://www.umassmed.edu/schifferlab/
>
>
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Received on Mon Apr 01 2024 - 13:00:02 PDT
