[gmx-users] [Fwd: deprotonated systeine]

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 21 23:43:20 CEST 2008

David van der Spoel wrote:
> 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”.

Without showing us your exact command line, we can only guess that you've not 
given the correct command.  Besides, the options for cysteine only apply to 
protonated cysteine or the disulfide form in most conventional force fields; 
these are the limitations of the force field.

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

Yes.  Consult the manual and wiki on how to do this.

> 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)

That choice is yours based on structural/biophysical data available for your 


>  Best regards
> Nedjoua Drici
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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