On Tue, May 25, 2010 at 11:58 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > > > Part of a residue I am parameterizing is a square planar metal
> > > coordination
> > > > complex. I have some questions about the improper torsions that LEaP
> > > chooses
> > > > to apply. For the purpose of discussion, I have simplified the
> structure
> > > so
> > > > that the central atom (a metal atom) is labeled C, and the
> coordinated
> > > > ligands are the points of a compass (clockwise N, E, S, W):
> > >
> > > > N
> > > > |
> > > > W - C - E
> > > > |
> > > > S
> > >
> > > > These are my improper parameters:
> > >
> > > > IMPR
> > > > E-S-C-W 0.2 180.0 2.0 These 2 impropers
> are
> > > > applied by LEaP
> > > > N-S-C-W 0.2 180.0 2.0 .
> > > > S-E-C-W 0.2 180.0 2.0 These 4 are not
> > > applied
> > > > by LEaP
> > > > S-N-C-W 0.2 180.0 2.0 .
> > > > S-W-C-E 0.2 180.0 2.0 .
> > > > S-W-C-N 0.2 180.0 2.0 .
> > >
> > > > I verified that the first two impropers are applied by examing .C in
> > > rdparm:
> > > > B 2901: 0.200 3.14 2.0 :25.E :25.S :25.C :6.W
> > > > (768,760,758,168)
> > > > B 2902: 0.200 3.14 2.0 :25.N :25.S :25.C :6.W
> > > > (776,760,758,168)
> > >
> > > > C is square planar; W and S are trigonal planar; N and E are
> tetrahedral.
> > >
> > > > ***From reading the list, I have gathered that assigning impropers is
> > > > complicated. Many references are made to LEaP recognizing "planar"
> > > > topologies and applying an improper (if parameters are given,
> otherwise a
> > > > warning is generated). How is the "planar" topology recognized?
> Simply by
> > > > finding tricoordinate atoms? Can you explain how LEaP decided to
> apply
> > > some
> > > > of these impropers to my tetracoordinate atom?
> > >
> > > Planar topology as such is not recognized by leap; as you
> > > have guessed it examines a list of tricoordinate centers
> > > to see if any of the permutations match an improper parameter.
> > >
>
> > Can you explain why LEaP assigned some impropers to C, a tetracoordinate
> > atom? Two impropers were applied with C as the 3rd/central atom. My
> > intuition is that it has something to do with the trigonal planar nature
> of
> > the S and W atoms.
>
> The central atom of any tricoordinate system is always the
> third one in the improper. You would have to read leap code
> to see how the tetracoordinate center is handled as multiple
> tricoordinate terms.
Ah, I see. This explains at least generally why this happens.
> It may even be worth a detailed look,
> adding print statements to the code, since this is not a common
> case.
>
This sounds like fun, but I might have to take a rain check.
Thanks for the information.
Robert
>
> Ideally I think leap might avoid cases like NSCE where 'bonds'
> superimpose, but I didn't think of this case when working on the
> code for impropers eons ago.
>
> Bill
>
> > > ***Additionally, looking at the N-S-C-W improper (2nd in the list
> above):
> > > > N-S-C looks like an unstable choice to define a plane, since the
> three
> > > > points are (should be) collinear. Even a slight deviation of C from
> the
> > > > plane would result in a large angle between the planes defined by the
> > > > improper. Could this be problematic?
> > >
> > > You might want to avoid such combos - it could call for unfortunate
> > > ripple effects as you create new atom types and add the other params
> > > for them though, so I'd try without doing this at first.
> > >
> > > I'll keep this in mind, but I think I've avoided this, for now. The W
> atom
> > is the only one of its type in this system.
>
>
> > > > ***Also, I realize I can add the other impropers to the prmtop by
> hand,
> > > but
> > > > can this lead to strange behavior from sander?
> > >
> > > Depends on how well you do it :-)
> > >
>
> > I'll try hard then. Thanks!
>
> > Robert
>
>
> > > Bill
> > >
> > > > The square planar structure of the coordination complex is
> represented
> > > > sufficiently well with or without these impropers, but I would like
> to
> > > > understand what's going on behind the scenes. Apologies if this has
> been
> > > > answered before, but I did a fairly extensive search of the mailing
> list
> > > > without coming across a satisfactory answer.
> > >
> > > > Cheers,
> > > > Robert Elder
> > > > PhD Candidate
> > > > University of Colorado - Boulder
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Received on Wed May 26 2010 - 17:00:03 PDT
