[gmx-users] [Fwd: deprotonated systeine]

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 21 20:56:11 CEST 2008

I work with a protein where 3 CYS redisidues make bond with a Zn atom by 
its SG atoms and HIS redisidue makes bond with a Zn atom by its NE2 in 
active site

I want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says 
on option of choosing Cys protonated state possibility but why that 
option not appearing while running “pdb2gmx” , just like for “Arg”, 
“His”, “Asp” and “Glu”.

Must i generate a specbond.dat entry for Cys-Zn  His-Zn linkage ?

And what type of histidine do I have to choose

0. H on ND1 only (HISA)

1. H on NE2 only (HISB)

2. H on ND1 and NE2 (HISH)

3. Coupled to Heme (HIS1)

  Best regards

Nedjoua Drici
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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