[Chimera-users] How to modify a structure to put some atoms in a plane....

Sergio Garay sergio.alberto.garay at gmail.com
Thu Sep 12 07:17:19 PDT 2013


Hi all

I'm trying to put a Nitrogen atoms of a Nitro group in the same plane that
a imidazol ring, but until now with no success. I've tried using modify
structure and changing the bond and geometry of the carbon to which the
Nitrogen is joined, but it did not work. I attached an image with the
problem. I've also tried to minimize the structure using AMBER ff (despite
I know that this ff is not appropriate for small organic molecules) but it
can fix the problem. May be I'm not clear enough so, I summarize: I want to
put the Nitro group in the same plane of a imidazol ring (look at the
picture, please). Any advice will be appreciated.

[image: Inline image 1]

Sergio


-- 
Sergio Garay
Dr. en Ciencias Biológicas
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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