From: Yarrow Madrona (
Date: Sun Apr 21 2013 - 17:49:21 CDT


I know this is a CHARMM question but I am having trouble finding
information on this.

I am wondering if anyone here has experience with HEME-cystiene Fe thiol
or Fe-HIS simulation. I recently build a parameter and top file with a new
residue "HEC" which is a combination of the HEME and cysteine as a single
residue. I took most of the HEME parameters from the CHARMM Heme streaming
toppar file.

Everything looks fine except the HEME seems to flex a little. Looks a
little like a "V" Maybe 140-160 deg instead of 180 degrees across the
heme. I have heard that there are some parameters to take from the PRES
SUL patch in the HEME topar streaming file. I have taken and modified the
relevant ones but I was wondering if anyone knows specifically, what would
cause the heme to be less than ideal planar.

Thank you for your help.

Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697