On Tue, 2014-03-04 at 18:42 +0200, Gmail2 wrote:
> Dear Dr. Jason,
>
> In my structure, a zinc is connected to the nitrogens of three
> histidines and a water. The structure should be simulated with Zn
> bound to three deprotonated (negative) histidines and a water. I am
> wondering what is the default net charge of histidine in Amber?
The answer was in my last reply as well as advice for how to deal with
your system. You will need to derive charges and force field parameters
for your metal center. You can use R.E.D. to do this or MCPB. I also
suggest working through the tutorial I provided to see how to create
custom residues.
Parametrizing your compound will likely take a fairly long time.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 04 2014 - 09:00:03 PST
