Hi Lin,
cis-transisomerization of a double bond cannot occur in a minimization. Is
your starting conformation really a cis-azobenzene? Does it have huge
clashes that might disrupt your structure? Unless you have very strange
parameters set, what you see will indeed not occur during a minimization
unless things go very wrong.
Check the atom types antechamber has set for your molecule and look up the
dihedrals that apply if you really have a double bond there (alternating
single-double bonds used to confuse older versions of antechamber, Im not
sure that is still a danger...)
Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Fri Apr 18 2008 - 21:15:39 PDT
