Cyclopeptide: connectivity between the first and last residues

From: List (zheng042003_at_yahoo.com)
Date: Mon Sep 29 2008 - 12:52:14 CDT

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Dear NAMD experts,

I have a question around running MD for a CYCLOPEPTIDE.   When the regular procedure was applied, after minization, the bond between the first and the last residues got broken.  I guess these two residues are not connected in the .psf file although they are geometry-wise.  I wonder if there is any way to specify the connectivity or apply any constraint, so that the first and last residues will remain bonded/connected throughout the MD simulation.

Any help will be greatly appreciated,

Shirley

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