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.
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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/>
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Received on Wed Jan 20 2021 - 17:30:02 PST