psfgen creates too many bonds in a distorted Fe4S4 cluster

From: Sibo Lin (
Date: Mon May 10 2010 - 22:50:00 CDT

I'm trying model a ferrodoxin protein with a distorted Fe4S4 cluster
( When I
try to create a psf file via VMD's psfgen commandline program, the
cluster comes out interconnected in the psf. Is there some way to
prevent this? I'm using topology and parameter files for Fe-S clusters
from Chris Chang's paper
(, but upon minimization
the Fe4S4 cluster collapses rather than remain somewhat cube-like. I
think the extra bonds that psfgen defines may play a role in this.


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