On Mon, May 24, 2010 at 6:06 PM, 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.
> ***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 Tue May 25 2010 - 09:30:19 PDT
