VMD-L Mailing List

From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Sun Apr 21 2013 - 17:49:21 CDT

Hello,

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