It seems that Dave Case's insight is important:
"The only invariant thing you can do with a torsion (proper or improper) is
to reverse it: ABCD == DCBA. All other permutations are different."
This jibes with the way the rest of Amber lines up impropers so that they
can be treated just like any other torsion. However, it seems I now have a
slightly different problem. In the topology that the student created,
which I have attached, it appears that there are BOTH proper and improper
torsions with atoms c3 na ca ca. I am reading the topology verbatim, and I
find the following dihedrals (without hydrogens):
23 24 25 26 c3 c3 n4 c3
23 24 25 27 c3 c3 n4 c3
23 24 25 28 c3 c3 n4 c3
...
22 1 4 8 c3 na ca ca
...
22 1 2 5 c3 na ca ca
...
22 1 -4 -2 c3 na ca ca
In the (abridged) list of dihedrals above, I have taken care to divide each
array index by three, add 1 if was positive, and subtract 1 if it was
negative. In this manner I am giving the atom numbers (first atom starting
at 1) of the atoms involved in various dihedrals, and making those indexes
negative if the topology is trying to tell me that the dihedral is an
improper. I then give the type of those same atoms, in the same order.
Note the final three dihedrals: these are the infamous "c3 na ca ca"
beasts. This exposes one vulnerability in mdgx parameter fitting, that
when it is confronted with a parm.dat file containing proper and improper
dihedrals with the same atom type sequence one will overwrite the other.
This may be my only problem, but that outcome seems like a long shot: when
I look at the way the TOPOLOGY itself has ordered the (22, 1, -4, -2)
dihedral (clearly an improper if you visualize those atoms in the PDB), the
atom typing is clearly not in alphabetical order. Let's posit the central
atom is ca: (c3, na, ca) is not alphabetical. Let's posit that the
improper dihedral should be reversed, per Dave Case's input: the sequence
would then na is the central atom, which is the correct if one looks at the
PDB (the nitrogen is central to the three carbons). However, the reverse
of the dihedral would then be "ca ca na c3" which is, again, not
alphabetical, unless I am supposed to take "a, b, c, ..., y, z, 1, 2, 3,
..." which doesn't seem to line up with the declarations I see in the
gaff.dat file (numbers go before letters in the ordering).
Anyone help sort this out? The fate of better small molecule force fields
may hang in the balance!
Thanks!
Dave
On Thu, Mar 24, 2016 at 9:53 AM, Brent Krueger <kruegerb.hope.edu> wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> _______________________________________________
> 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 - 08:00:04 PDT
