Re: Heme - Cysteine link

From: Elsa F. Sousa Henriques (Henriques_at_fias.uni-frankfurt.de)
Date: Tue May 09 2006 - 09:09:33 CDT

I don't think the top_all27_prot_lipid.inp has any patch for linking a
cysteine to the heme's Fe atom (it has one for linking a histidine
though). Also, I believe you have to apply the patch residue FHEM to
your heme to get rid of some unwanted auto-generated angles, otherwise
the planarity around Fe will get very distorted when you run a
simulation.

Hope it helps,

Elsa

Quoting Muhittin Emre Özdemir <muhittinozdemir_at_gmail.com>:

> Hi everyone,
>
> I am rying to simulate a protein with heme. I am able to create all the
> files necessary for simulation. but I noticed something odd in the
> simulation I made. There should be a link between a S atom of cysteine and
> Fe atom of heme, which is why i am asking help for. The link doesn't exist.
> I guess there is something wrong with the final pdb and psf files. This is
> the script I use for creating them:
>
> package require psfgen
> topology top_all27_prot_lipid.inp
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> pdbalias residue HEM HEME
> segment C {pdb cyp1.pdb}
> segment H {pdb hem1.pdb}
> coordpdb cyp1.pdb C
> coordpdb hem1.pdb H
> guesscoord
> writepdb cyp2.pdb
> writepsf cyp2.psf
>
> Any ideas?
>
> Thanks in advance for your help...
>
> --
> Muhittin Emre Özdemir
>

-- 
Elsa Henriques, Ph.D.
Frankfurt Institute for Advanced Studies   Tel: +49 (0)69 798 47502
Max von Laue Str. 1, room 1.215            Fax: +49 (0)69 798 47611
60438 Frankfurt am Main, Germany        E-mail: 
Henriques_at_fias.uni-frankfurt.de
          http://www.fias.uni-frankfurt.de/home/solovyov/MEMBERS/henriques.html
.-.   .-. .-.   .-. .-.   .-. .-.   .-. .-.   .-.
X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X.-.   .-.
\|||X|||/ "There is no gene for the human spirit" |||\ /|||X
  `-' `-'  \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/
            `-' `-'   `-' `-'   `-' `-'   `-' `-'   `-' `-'
in Gattaca(1997)

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:28 CST