Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 26 09:27:05 CEST 2009

Hi Nehme,

> Also, in our zinc finger models, the zinc plays a structural role and it is
> not implicated in DNA recognition. Furthermore, I will read your paper and
> the references. I looked in the Literature and from NMR studies/X-ray and MD
> done on zinc fingers containing a zinc ion coordinated to 4 cysteines. It
> seems that these cysteines are deprotonated and the remaining negative
> charges are stabilized by nearby positively charged side chains of arginines
> or lysines.

It's hard, although not impossible, to assess the protonation state of
such a center experimentally. Mind that crystal structures and NMR
structures also use force fields and predefined topologies to model
the structure. That means that you will only get out what you put in.
If you set some group to be deprotonated while it should be
protonated, this may be hard or even impossible to track down. You may
still get a reasonable fit to the experimental data. For such issues
Xray/NMR are not the best means. Note that I'm not saying you're
wrong, but you should justify your choices.

> I tried to use CHARMM forcefield, but every time I had the 4 cysteines
> protonated, the coordination bonds removed and the parameters for zinc not
> assigned.
> How can I solve this issue?

In Gromacs you can use the file specbond.dat to define special bonds.
Have a look at http://wiki.gromacs.org/index.php/specbond.dat and
search the archives for more information.



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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