OK, good to know the history. Thanks Bill!
On Thu, Mar 24, 2016 at 2:01 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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 - 23:30:04 PDT
