On Mon, Nov 21, 2022 at 12:53 PM He, Amy via AMBER <amber.ambermd.org>
wrote:
> Dear Amber experts,
>
> I am using Amber 20 and I was trying to parameterize a nonstandard
> residue. At first, I used antechamber and let it look up parameters from
> parm10.dat and gaff2.dat. Then, I found in the output frcmod files that,
> the parameters for a dihedral might need some further refinement by
> comparing to QM calculations, as it returned a very large “penalty score”
> (>500)..
>
> I would really appreciate it if you could help me with the following
> questions, about refinement of dihedral parameters by QM calculations:
>
> 1.
> A dihedral appears as X1-X2-X3-X4 in the frcmod file, and my dihedral of
> interest contains X3 that is bonded to three different X4, so the rotation
> of X2-X3 is under the regulation of three dihedral terms. If that is the
> case, which X4 should I choose to perform a QM scan?
>
are all of the X4 the same atom type, or different?
>
> 2.
> What should be the main objective of the fitting: Should I aim at
> reproducing the torsional profile, or the conformational energies of a
> variety of conformers?
>
these should be the same thing, unless there are other dihedrals involved
as well that need correction. doing the whole profile may be needed if the
barrier height is important to you.
>
> 3.
> What might be a good algorithm for the fitting, if I am expecting three
> formulas (each might contain one or two functions, and they are correlated)
> to parameterize this dihedral?
>
I am not sure what you mean by formulas and functions (and how they are
different)
>
> Any comments, suggestions would be greatly appreciated.
>
>
> Many Thanks,
> Amy
>
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
> he.1768.osu.edu
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Received on Mon Nov 21 2022 - 10:00:03 PST
