On Thu, Mar 24, 2016, Dave Cerutti wrote:
> 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?
Yes: alphabetical order on atom type for A,B,D; break ties by using the atom
name. (Easier: sort alphabetically on a key formed by the atom type followed
by the atom name.)
>
> 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?
Above is wrong: the fact that the order of A,B and D matters is the origin of
requiring them to be an alphabetical order. The only invariant thing you can
do with a torsion (proper or improper) is to reverse it: ABCD == DCBA. All
other permutations are different.
....dac
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Received on Thu Mar 24 2016 - 04:30:05 PDT
