CCL: CCL Macromodel conformation search
- From: Eric Bennett <ericb(_)pobox.com>
- Subject: CCL: CCL Macromodel conformation search
Sent to CCL by: Eric Bennett <ericb(_)pobox.com>
Was wondering if it was possible to do a
conformational search with Macromodel
where one is changing the puckering in a five membered ring.
You can search ring conformations using either (a) the
LMCS [for a few
hundres atoms] or LMC2 [for very large systems] directives or (b) RCA4
and TORS directives in the command file. LMCS is easier and tends to
more efficient for large rings, although it may not matter for a five
membered ring. If you are setting up the job in Maestro, then under
"CSearch" tab of the Conformational Search window you need to
'Method' that includes "Low Mode". If you are searching a
molecule then you probably either want "Mixed MCMM/Low Mode"
(if you are
defining other torsions to be searched) or "Pure Low Mode"
(if you are
not defining torsions).
LowMode distorts the molecule along some cominbation of its calculated
vibrational modes and will perturb any atoms that are not
to my consternation it *will* try to move atoms which are
compared to simple torsion searching, LowMode is also more likely to
flip chiral centers so be sure to define chiral centers if your
Some LMCS references:
J. Comput. Chem. 20(15), 1671-1684 (1999)
JACS 118(21), 5011-5019 (1996)
Eric Bennett, Center for Drug Design, U of Minnesota
I am not a vegetarian because I love animals. I am a
vegetarian because I hate plants. - A. Whitney Brown