Hi Anthony,
> On Jul 23, 2021, at 10:38 AM, Anthony Nash <anthony.nash.ndcn.ox.ac.uk> wrote:
>
> In answer to my own question concerning multiple metal ions in a protein...
>
> For each metal ion (x2 Zinc, x4 calcium), I prepared an "original_pdb" file that contains the protein and only ONE metal ion. Thus, I have a "small model" pdb and QM input file for each of the metal ions.
>
I think only for the two zinc metal ions you need to do such a kind of thing, for Ca2+ ions I would recommend you to use the nonbonded model, for which case you do not need to do such a kind of thing. You can check this webpage for how to use the nonbonded model: http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm>. And if the two Zn2+ metal sites are identical, actually you can just parameterize one of them, and use the same parameters for the other site.
> I also found that my "original_pdb" file had incorrectly protonated histidines (HIP when it should be HID). I suspect this was from H++ webserver.
>
Yes, H++ will not recognize the metal ions when determining the protonation states of the amino acids, so sometimes manual adjustment of the protonation states of metal ligating residues are necessary. You can check the sub-step 2) under step 1 in this tutorial for an example: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>.
> Pengei, thank you for your help and for the number of published and web-based resources I've been using.
>
Glad these works can serve the community.
Pengfei
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Received on Fri Aug 06 2021 - 16:30:02 PDT
