AMBER Archive (2008)

Subject: Re: AMBER: running minimisation on cis-azobenzene

From: Thomas Steinbrecher (
Date: Mon Mar 31 2008 - 15:14:17 CDT

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...)



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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