[gmx-users] HG at active site of alcohol dehydrogenase

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 1 13:24:15 CEST 2007

Salaam Aleikum Karim,

This is a non-trivial issue. Put simply, you need to parameterize the
Zn bound cys and his residues and add these to the .rtp database of
your choice and you have to add the Zn-His and Zn-Cys connections to
the specbond.dat file (search the archives). I hope you have
experience with MD simulations and with parameterization, otherwise I
would strongly suggest to chose another subject.
Also, be aware that there is still quite a deal of uncertainty about
the protonation states of Zn-bound His _and_ Cys in ADH. This is not
something to burn your hands on if you're new to the field.

Best regards,


On 5/1/07, Mahnam <mahnam at ibb.ut.ac.ir> wrote:
> In God We Trust
> Hello Dear GMX users
> I want to do MD simulation on alcohol dehydrogenase.When I make topology
> file for this protein , gromacs uses cysH for cys that is connected to Zn in
>  active site. How can I make topology file without HG.
> pdb2gmx doesn't have option for CYS without HG and also I can't use -ss
> option.
> I addition I changed HG to DUM and put 0 for its mass, but grompp don't
> accept mass of 0 for this DUM atom.
> Many thanks in advance for your help and your reply.
> Yours truly
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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