Hi Abhilash,
Yeah, I have seen such a metal site before. You probably need to parameterize a deprotonated HIS residue (no proton on delta and epsilon positions) by yourself first. You can check an example here about how to parameterize a non-standard amino acid: http://ambermd.org/antechamber/pro4.html <http://ambermd.org/antechamber/pro4.html>. And then you need to prepare a mol2 file for it, and put the name of the mol2 file after the naa_mol2files variable in the MCPB.py input file.
Hope it helps,
Pengfei
> On Jun 4, 2019, at 6:02 AM, Abhilash J <md.scfbio.gmail.com> wrote:
>
> Hi Everyone,
>
> I am trying to generate AMBER parameters for a protein which has two ions (Zn and Cu) in its active site.
> Both ions share a common histidine which is doubly deprotonated (no proton on delta and epsilon positions).
> I am trying to do this using MCPB.py but am getting error as there is no doubly deprotonated Histidine in AMBER forcefield.
> Please suggest how to go about this.
>
> Regards
>
> Abhilash
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Received on Sat Jun 15 2019 - 18:00:02 PDT
