How to make a virtual bond?

From: patrick wintrode (
Date: Wed May 24 2006 - 13:27:24 CDT

Hi all.

I'm trying to set up a complicated simulation. Essentially, I want to use NAMD to look at how a protein responds when one of its loops is cleaved by a protease. My plan is to remove the peptide bond in the original pdb file (adding appropriate patches to the new N and C termini), then use restraints in order to mimic the presence of the bond. After the system has equilibrated, I'll turn off the restraints and watch how the system evolves in response.

My questions:

1) what's the best way to prepare the modified pdb file? I tried doing it with SwissPDB, but when I used the resulting modified PDB file with PSFGEN, the new cleaved ends caused a fatal error.

2) does anyone know of the best place to look for how to set the restraints to mimic the presence of a peptide bond as accurately as possible?


Patrick L. Wintrode
Assistant Professor
Department of Physiology & Biophysics
Case Western Reserve University
Cleveland, OH 44106

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