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
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