Sorry. HIS is HIE in Amber. And It is neutral.
Ahmet Yıldırım
4 Mar 2014 tarihinde 18:51 saatinde, Jason Swails <jason.swails.gmail.com> şunları yazdı:
>> 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 - 09:30:04 PST
