VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 22 2013 - 04:48:09 CDT

two comments:

1) have you made some test calculations with the regular heme residue
as provided in the parameter set to have a reference to compare to?

2) parts of molecules are usually held flat through improper
dihedrals. have you checked whether they are exist where needed and
have assigned parameters for your custom residue? again, it can be
extremely helpful to compare to "vanilla" reference.

axel.

On Mon, Apr 22, 2013 at 12:49 AM, Yarrow Madrona <amadrona_at_uci.edu> wrote:
> 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
>
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.