Subject: Conformational Search in BatchMin

From: [email-masked] (Peter Shenkin)
Date: Thu, 9 Jun 94 12:31:49 -0400

Several people have asked me for more details, so I thought it best
to post to the list.

We supply a number of conformational search methods -- systematic
as well as Monte-Carlo -- and all can be set up from the MacroModel
front end.  With automatic setup, the program finds the variable
torsions and ring opening/closure bonds, and configures the search.
The user can then examine and modify the setup if desired.  Things
that can be altered include the following, but, to be honest, the
automatic setup does a pretty good job on most of them: 

	the list of torsions to be varied
	symmetry when discarding duplicates (e.g., rotating an
	 unsubstituted phenyl ring 180 degrees, or reversing the
	 ordering of the atoms in an n-alkane). 
	which atoms to use when comparing structures
	energetic threshold above the lowest minimum found for
	 discarding high-energy structures
	degree of geometric similarity required for two structures
	 to be considered identical
	various minimization parameters to alter the extent of
	 refinement during the search
	number of steps (starting geometries) for the search
	
We find that usage-directed Monte Carlo search is best.  In this
method, structures previously found are used as starting conformations
for Monte-Carlo moves, with a heavier weighting given to the LEAST
frequently found structures.  This increases the chances of finding
new basins of attraction.

Conformational search can be run in network-distributed fashion over
a "farm" of (possibly heterogeneous) workstations.  Search can also be
run in the context of the GB/SA solvation model;  the energetics then
reflect relative conformational energies in the chosen solvent.

In the latest release of the code, 4.5, which we've just started
shipping, we supply some new facilities to help determine when
a search is complete, and to initialize ("seed") a new search from
the results of an old one, in case one suspects that the old search
was not complete.

The new facilities include periodic reports of how many times
low-energy minima were found in the search so far.  These reports 
can also be triggered on demand from a running process.  The reports 
also include information on whether all structures found so far 
minimized to convergence, so that the user can determine whether 
a follow-up run to perform a more extensive minimization in warranted.  

Finally, the number of times each minimum was found is preserved in 
the output structure file.  If a new conformational search is 
subsequently performed using the output of a previous run as a "seed",
the energies and numbers of times found are used to initialize the usage-
directed algorithm.

	Hope this helps,
	 -P.
********** After the revolution, everyone will have a home page... **********
Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ.,
New York, NY  10027;     [email-masked];     (212) 854-5143
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