How to calculate energy?

From: Huayue Li
Date: 2011/10/15

Dear all,

I obtained 20 peptide models (with lowest energy) calculated by CNS program. Now I want to make a table for structure statistics, but I don't know how to calculate E_bond E_angle E_improper E_vdw E_NOE E_cdih E_total , r.m.s. deviation from experimental constraints, and r.m.s. deviations from idealized geometry.

Where can I get these information? Just from the peptide pdb file output by CNS, or using another software? And what is idealized geometry?

 

Thanks!

Huayue Li, Ph. D

College of Pharmacy
Pusan National University
Geumjeong-gu, Jangjeon-dong
Busan 609-735, Korea

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From: Boaz Shaanan

This should all be in the CNS output file for each cycle.

          Boaz

  

Boaz Shaanan, Ph.D.                                        
Dept. of Life Sciences                                     
Ben-Gurion University of the Negev                         
Beer-Sheva 84105                                           
Israel