[AMBER] AMBER-cis-trans conversion

From: Gözde YALÇIN <yalcingozde88.gmail.com>
Date: Tue, 21 Jan 2014 17:19:31 +0200

I did minimization with this molecule:
N-CH2-CH-CH-CH2-N
N-c3-c2-c2-c3-N
After 1000 steps of minimization, the trans sp2 carbons(c2) convert to cis
conformation. I couldn' t understand what can be responsible for this
situation? Where I did a mistake?Can you help me to solve this
problem.Thanks for your relevancy...

-- 
Gözde YALÇIN
Research Assistant
Rize Recep Tayyip Erdogan University
Faculty of Engineering
Bioengineering Department
53100 Rize-Turkey
Ph.D. Student in Biotechnology
Ankara University
Biotechnology  Institute
06110 Besevler/Ankara-Turkey
05065055074
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Received on Tue Jan 21 2014 - 07:30:03 PST