> 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.
> ***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.
> ***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 :-)
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 Mon May 24 2010 - 17:30:03 PDT
