Heme - Cysteine link

From: Muhittin Emre Özdemir (muhittinozdemir_at_gmail.com)
Date: Tue May 09 2006 - 04:06:46 CDT

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
writepdb cyp2.pdb
writepsf cyp2.psf

Any ideas?

Thanks in advance for your help...

Muhittin Emre Özdemir

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:02 CST