Hi all,
I am working on parameterizing NADH for an updated tutorial on RESP and
Paramfit, but I'm running into problems with how to obtain an optimized
structure. I downloaded an "ideal" solvated structure from the PDB and ran
a B3LYP optimization in gas phase according to the procedure outlined in
tutorial A1. The resulting structure is folded up and quite different from
the more realistic solvated structure, so I was wondering how to proceed.
Running a RESP on an unrealistic structure doesn't seem like it would give
sensical results.
Is there any sort of "industry standard" for approaching this problem? Ross
Walker suggested conducting the optimization step using DFT with implicit
solvent to perhaps obtain a better structure.
Thanks,
Robin Betz
UC San Diego
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Received on Wed May 02 2012 - 16:00:02 PDT
