AMBER Archive (2008)

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

From: Thomas Steinbrecher (
Date: Tue Apr 08 2008 - 15:37:39 CDT


if the central bond in your system is ca-ne-nf-ca and you have specified a
ca-ne-nf-ca dihedral of 100000kcal/mole with correct phase and
multiplicity in a frcmod that you have sourced into leap before writing
the prmtop file and your initial system conformation is a cis-azobenzene
with reasonable geometry, then you should not get a trans-conformation
after minimizing.

Therefore, if you do get a trans-azobenzene, I guess one of the above
assumptions is not true. Which one that is is hard to tell without knowing
what exactly you did to set up your system.



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