Re: [AMBER] ZAFF force field

From: Pengfei Li <>
Date: Fri, 26 Feb 2021 17:12:51 -0600

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 <>.

Hope it helps,

> On Jan 20, 2021, at 7:09 PM, Tabassum Khair Barbhuiya <> 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
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Received on Fri Feb 26 2021 - 15:30:02 PST
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