While we are here talking about impropers, can someone explain to me why we
leave two of the improper dihedrals in TRP undefined (C*-CN-CB-CA
and NA-CA-CN-CB)? I presume this is obvious to some in the group and that
they are just unnecessary because things stay appropriately planar without
them, but I've always been curious about this.
Thanks,
Brent
On Thu, Mar 24, 2016 at 7:23 AM, David A Case <david.case.rutgers.edu>
wrote:
> 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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--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Thu Mar 24 2016 - 07:00:03 PDT
