RE: HEME and Cystein instead of His

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Wed Nov 23 2011 - 14:33:39 CST

Dear Raul,

I am also working with a protein with a heme group linked to a cystein.

In my case I have used the follwing tcl script and it works:

package require psfgen
topology MOL_top_all27_ISM.rtf

# Read protein coordinates from PDB file
pdbalias atom ILE CD1 CD

# alias residue H6M H6ME
segment U {pdb ttt_prot_1.pdb
first NTER
last none}
segment V {pdb ttt_prot_2.pdb
first none
last CTER}
segment H {pdb ttt_HEME_2.pdb}

patch link U:193 H:900
patch link H:900 V:195

segment B {pdb ttt_H4B.pdb}
segment W {pdb ttt_water.pdb}
segment A {pdb ttt_MOL.pdb
first none
last none}

coordpdb iNOS_prot_1.pdb U
coordpdb iNOS_HEME_2.pdb H
coordpdb iNOS_prot_2.pdb V
coordpdb iNOS_H4B.pdb B
coordpdb iNOS_water.pdb W
coordpdb iNOS_MOL.pdb A

# (9) Guess missing coordinates
guesscoord

# (10) Write structure and coordinate files
set tmp tmp
writepsf $tmp.psf
writepdb $tmp.pdb
writepsf ttt_charmm.psf
writepdb ttt_charmm.pdb

I also have good paramenters for the heme-cys system parameterized by Cho et al. (Cho, K.-B., Derat, E. & Shaik, S. JACS 129, 3182-3188 (2007))
Send me a mail if you are interested or contact the authors. They will send you the parameters for sure...

Regards,

Bruno

...................................................................................................................................................
Bruno L. Oliveira
Radiopharmaceutical Sciences Group
Chemistry Department , ITN
http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
http://www.boliveira.com
________________________________
De: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] em nome de Raul Araya [arayasecchi_at_gmail.com]
Enviado: quarta-feira, 23 de Novembro de 2011 19:10
Para: namd-l_at_ks.uiuc.edu
Assunto: namd-l: HEME and Cystein instead of His

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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