Re: HEME and Cystein instead of His

From: Aron Broom (
Date: Wed Nov 23 2011 - 14:02:42 CST

I've previously made new molecules for CHARMM. I don't know if they
formats have changed, but it used to be that the topology and parameter
files were human readable. If this is the case, you could just take your
HEME-His definition and change it around to be HEME-Cys. Obviously you
might need to consider the various parameters for the atoms under this new
environment, maybe using a higher level of theory.

In terms of autopsfgen I'm not sure what the intended usage method is, but
you stick your new HEME-Cys topology and parameters inside the existing
topology and parameter files and rename them, you can pass those topology
and parameter files to autopsfgen and it will work fine.


On Wed, Nov 23, 2011 at 2:10 PM, Raul Araya <> wrote:

> Dear NAMD users
> Im interested in simulating a cytochrome protein whos HEME group is linked
> to a CYS residue and not to a HIS.
> I have found on the CHARMM topology files patches for linkinf the HEME
> group to a HIS...
> Does anybody nows or have the patch to link the HEME to a CYS?
> I heard about a patch called FE2S that is supposed to link the HEME to a
> CYS but I have not been able to find it....
> How are the other HEME related patches used with autopsfgen?
> Any help will be appreciated.
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.

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