Thanks to David Cerutti for the warm help.
>has over 5000 angle parameters for different chemical environments, and
those are all done at the B3LYP/6-31G* level
>both parabolas, positioned with their respective minima on either side of
the minimum that you anticipate the angle to have
I understood that AMBER/GAFF examined thousands of molecules to
statistically get a reliable parameter. The method for angle fitting is
quite interesting. Meanwhile, I remember that at a month ago, someone asked
about "is the force constant derived from a mass-weighted Hessian", and the
answer was yes.(
http://archive.ambermd.org/201602/0129.html) I'd like to
ask, for a certain mmolecule, how do we derive the force constant from a
mass-weighted Hessian?
> Fitting dihedral terms
For dihedral fitting of X-ca-ca-X, the source of it wrote "intrpol.bsd.on
C6H6", so I'm guessing it's parameterized based on benzene. I understand we
should fill in the wildcard X with actual atom types, and then, as the GAFF
paper wrote, we do a PES scan about the torsion angle. However I feel it
not possible to rotate a ca-ca bond in benzene? Is there any alternative
way to parameterize dihedrals if the dihedral itself is not easy to change?
I'm very grateful for the introduction about your epic work on mdgx while
unfortunately I'm not living in US. Looking forward to read your great
paper once it's available.
Also thanks to Thomas Cheatham for the clarification and the very helpful
suggestion. The fact that AMBER balanced and adopted OPLS idea of vdW is
truly important. I will go back to read OPLS and these earlier papers
carefully.
WANG, Ruixing
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Received on Wed Mar 16 2016 - 02:30:06 PDT
