Subject: complex geom calcn protocol

From: Goutam Das <[email-masked]>
Date: Mon, 4 Jan 1999 20:15:55 -0600

A little over  a week ago, I posted a question regarding a protocol for
calculating complex geometry and eventually the global minima.  Here is my
original query and the responses.  I  thank everyone who responded .
I wonder whether there are protocols (besides MD sim) for calculating
geometries (ab initio/semiempiric/molmech) of  minima's and finally glob
minimas  for pairs of simple molecules. If there are, I would deeply
appreciate if anyone could kindly point me to good references.  Normally I
optimize geom's of both mol's, then freeze the crd's of each and then move
one relative to another and then relax all constraints, guessing inital
geoms by intuition--I am sure I  miss a lot of conf's and maybe certainly
the glob min (although I understand that there is no guarantee that any
particular method could give the global min).  However, there should be a
much better & efficient subroutine.

If you have a MD program you can probably use the simulated annealing protocol
where you slowly cool your system until it freezes in. If you do it very slow
(a few ps) you will probably find the global minimum, if you do it fast
you will find other minima too. The method is used a lot in refinement but
useful for simple conformational searches too.

GROMACS implements the method in MD simulations.
http://rugmd0.chem.rug.nl/~gmx

Groeten, David.
________________________________________________________________________
Dr. Ir. David van der Spoel	Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

You sure do miss  a lot of conformations. However the problem is non
trivial and to my knowledge has not been solved for an arbitrary shaped
molecule. If you think about it for a moment you will realize that there
are 6 degrees of freedom for the interaction of two molecules(imagine
one fixed at the origin and the other rotating and translating about
it). This already gives you millions of conformations to check. Add to
that the internal degrees of freedom for rotation about single bonds and
the problem becomes intractable.
The best we have done here is a Monte Carlo simulated annealing of a
dimer with internal bond rotations. It works well, but there is no
guarantee we have found all the important local minima when the number
of internal bond rotations is large.
JERRY

--
**************
Jerry Perlstein
Center for Photoinduced Charge Transfer
Department of Chemistry
University of Rochester
Rochester,NY 14627-0216
Tel: (716)275-2511
FAX: (716)242-9485
[email-masked]
http://www.chem.rochester.edu/~stc/perlstein.html

GOUTAM  DAS, Ph.D
BETZDEARBORN (A division of Hercules)
PO BOX 4300, 9669 GROGANS MILL ROAD
THE WOODLANDS, TX 77387-4300
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