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?
Ahmet Yıldırım
4 Mar 2014 tarihinde 15:17 saatinde, Jason Swails <jason.swails.gmail.com> şunları yazdı:
>> On Tue, 2014-03-04 at 11:12 +0200, Ahmet yıldırım wrote:
>> Dear users,
>>
>> How can I get/find the Amber force field parameters for the deprotonated
>> histidine?
>
> Histidine has 3 major protonation states at biological pHs.
> Single-protonated at the delta- or epsilon- positions and
> double-protonated (protonated at both). The first two states are
> neutral, the third is positively charged.
>
> You have to change the residue name of HIS to HIE or HID for epsilon- or
> delta-protonated histidine, respectively (HIS is interpreted as HIE).
> To get the double-protonated form, change the residue name to HIP.
>
> A fully deprotonated histidine (no protons on either Ne or Nd) would
> need to be parametrized (mainly just the charge derivation). See
> http://ambermd.org/tutorials/advanced/tutorial1_orig/ for example. Note
> that this is a _highly_ unusual form of histidine that would only be
> present at extremely high pHs (I've never seen the pKa value for the
> second imidazole H since it rarely [ever??] comes off).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 04 2014 - 09:00:02 PST
