structure breaking

From: ipsita basu (ibasu788_at_gmail.com)
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

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