Hi Aravind,
The two HIS residues in Center ID 4 are HID residues. For your case, I would suggest you to deal with the metal site which has 2 CYS and 2 HIS (1 HIE plus 1 HID) using MCPB.py, you can check this tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Pengfei
> On Dec 7, 2021, at 7:38 AM, Aravind R <aradrive1.gmail.com> wrote:
>
> Dear Amber Users,
> I am trying to model a protein with two Zn ions (One coordinated with 4
> CYS whereas the other coordinated with 2 CYS and 2 HIS (one in HIE and one
> in HID protonation states)). I saw that Zn with 4 CYS can be modelled using
> Center ID 1 from ZAFF. The closest I can find for other Zn is Center ID 4
> which when used shows, lengths, angles & torsions are missing for
> interactions containing two Zn.
> What is the best way to model this system?
> Any help is appreciated.
> Regards,
> Aravind R
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Received on Fri Dec 17 2021 - 17:30:02 PST
