Hi
I was looking into the paramfit program to get a few dihedral parameters, and had a few questions that I haven't found answers to in the manual or mailing list.
1) The molecule I am parameterizing has 60 atoms so I was going to try a smaller fragment. Since electrostatic interactions are calculated in 1-4 interactions, are there any considerations for RESP charges? I could use the entire molecule and lower the basis set.
2) The Amber force field will have a different set of equilibrium bond lengths and angles than the QM calculations. Is this accounted for in the 'K' term? Shouldn't a geometry optimization be performed in amber with the ff with the dihedral angle fixed, then a QM optimization calculation with the dihedral angle fixed? From the examples in the manual, it looks like the energies are just calculated using both MM and QM and compared.
Any help would be appreciated!
Thanks
Cody
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Received on Thu Apr 18 2013 - 11:00:02 PDT
