Re: [ccp4bb] How to calculate energy?

[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                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Huayue Li [lihua...@naver.com] Sent: Saturday, October 15, 2011 5:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to calculate energy? 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 Ebond Eangle Eimproper Evdw ENOE Ecdih Etotal , 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 Tel: +82-51-510-2185