Re: How to make a virtual bond?

From: Peter Freddolino (
Date: Wed May 24 2006 - 17:48:35 CDT

Hi Patrick,
for 1), we probably need a more detailed description of the error you
get. Normally VMD plays nicely with preparing psfgen/namd input, but
there's no reason I can think of that SPDBV wouldn't work.

For 2), what you might just want to do is prepare 2 psf files, one of
which actually does have a bond there. There's no technical problem in
switching psf files between simulation sas long as they have they same
number of atoms.


patrick wintrode wrote:

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

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