I'm posing this to the reflector in the hopes of a faster response. I've
had a student come to me with a parameterization question, and I'd like to
help him, but mdgx is choking when it cannot find an improper torsion with
the ingredients "c3 na ca ca." Nonsense, I said, this is right there
in the gaff.dat file we're referencing. However, the problem seems to be
that the improper is "ca-ca-na-c3" because of the naming conventions for
impropers. It seems that for an improper dihedral with atom types A, B, C,
D, the third atom type is the central atom, and that the first, second, and
fourth atom types should then be given in alphabetical order. I even have
a function, from years ago when I was writing this section of mdgx, which
enforces the alphabetical ordering of impropers.
1.) Can anyone tell me a little more about the origins of this convention,
or at least assure me that I'm doing the right thing in enforcing it?
2.) Can anyone confirm that, for any atom types A, B, and D, an improper A
B C D is equivalent to an improper D B C A and also B D C A, or any other
permutation that leaves C in position 3?
Thanks!
Dave
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Received on Wed Mar 23 2016 - 23:00:03 PDT
