structure breaking

From: ipsita basu (
Date: Tue Jul 27 2010 - 00:36:35 CDT

Hi all,
         I am running namd using NPT having system peptide embedded in
lipid bilayer. I have the peptide with N and C terminal capped with
formyl and ethanolamine . But during the simulation run the two capped
groups are breaking from the peptide. Before simulation run I had
restraints on peptide backbone.

Can you please suggest me what should I do to solve the problem. Thank you.

Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:20 CST