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
Hi Nehme,
I've did simulations on TRAIL, which also contains a zinc-finger
domain, involving three cysteines and a chloride ion. But it's not so
simple. Luckily the exact parameters seemed not that vital, as the
zinc apparently functions to keep the three subunits together and was
in any case not
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields
for that type of complexes (the zinc ion is coordinated to 4
deprotonated cysteines)?
I need to do some molecular minimization and dynamics including the
nucelic acid sequence.
Looking for some help.
Thank you.
Nehme El Hachem wrote:
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields for
that type of complexes (the zinc ion is coordinated to 4 deprotonated
cysteines)?
The first step is probably to search in the literature for anything similar.
Has anyone attempted such
Hi,
Have a look at
http://wiki.gromacs.org/index.php/Parameterization
and
http://wiki.gromacs.org/index.php/Exotic_Species
Next to that, also consider that you are talking about a site with -2
formal charge (ZnS4)2-. How likely is that? From QM studies, it seems
much more likely that there are
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