Hello,
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?
***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?
***Also, I realize I can add the other impropers to the prmtop by hand, but
can this lead to strange behavior from sander?
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 - 17:00:04 PDT
