> 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?
We had to come up with a convention when we switched from explicitly defined, residue-based impropers to topologically-applied parameters, and Peter Kollman made the final call on the convention. I believe I raised the issue, since it arose in the work on leap and validating the new code against the old. You are doing the right thing in enforcing it in that consistency seems valuable.
Note that this form doesn't work for nonplanar impropers because placement is ambiguous when there are duplicate atom types. We decided to kick this problem down the road.
> 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?
I suspect the forces on the atoms in a given conformation might be
different with different ordering of the terms, but the goal of
enforcing planarity over time would be achieved either way.
Bill
On 3/23/16 10:42 PM, David 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?
>
> 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 - 23:30:03 PDT
