From: Sławek Orłowski (bigman_at_phys.uni.torun.pl)
Date: Tue May 09 2006 - 08:20:50 CDT
Muhittin Emre Özdemir wrote:
> 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
Hi,
Your system is ok. You should look into a topology file. There are
several patches. For example PHEM:
PRES PHEM 0.00 ! Patch for HEME to His link.
! Patch residues must be 1-HIS, and 2-HEME.
If there is no patch for Cys to Heme link, you have to create it.
Best regards,
Slawek Orlowski
Theorethical Molecular Biopysics Group
Nicolaus Copernicus Univ. Torun
Poland
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