AMBER: Questions toward Azobenzene

From: Chih-Ying Lin <>
Date: Thu, 27 Mar 2008 21:23:40 -0700

Can N=N double bond rotate freely?
Can N=N double bond rotate freely under minimisation?

I am using Amber to run the cis-azobenzene minimisation. There are two states for running the minimisation.
Minimisation Stage 1 - Holding the solute fixed => visually, it is still a cis-azobenzene
Minimisation Stage 2 - Minimising the entire system => visually, it become a trans-azobenzene, but still have different
structrure with real trans-azobenzene

I don't know how this happened after 2nd minimisation.

Any ideas about this?


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Apr 18 2008 - 21:14:38 PDT
Custom Search