Hi Tabassum,
Sorry for the late reply. I was busy with moving in past weeks. For your case, ZAFF was not able to handle such case because your case has a different chemical environment, I would suggest you to parameterize the metal site specifically using MCPB.py: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Hope it helps,
Pengfei
> On Jan 20, 2021, at 7:09 PM, Tabassum Khair Barbhuiya <tabassumkhair.barbhuiya.hdr.qut.edu.au> wrote:
>
> Hello Team,
>
> I have some query for MD simulation of metalloproteins interaction with the ligand molecule e.g in case of PDB code: 5MJN. Here the Zn is coordinated with three of the amino acid "His" and one Nitrogen from the ligand molecule. So in such case can we treat ligand N is "His" in ZAFF force field as per the tutorial with metal centre type Zn-HHHH or shall we consider a separate force field. If in case Zinc is coordinated with the ligand Oxygen atom with (S=O bond) , can we treat it as HOH as metal centre type Zn-HHHO or shall we need to replace with water.
>
> [cid:image003.jpg.01D6EFE5.D7F3D9C0]
>
>
> Many Thanks,
> Tabassum Khair | PhD Student
> CARP - Cancer & Ageing Research Program
> Institute of Health and Biomedical Innovation | Queensland University of Technology
> Level 5| Translational Research Institute | 37 Kent St | Woolloongabba QLD 4102
> E: tabassumkhair.barbhuiya.hdr.qut.edu.au|<mailto:tabassumkhair.barbhuiya.hdr.qut.edu.au%7C> Web: www.carp.org.au<http://www.carp.org.au/>
> [cid:image006.png.01D6EFE5.D7F3D9C0]
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Received on Fri Feb 26 2021 - 15:30:02 PST
