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?
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?
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?
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 - 10:00:02 PST
