[AMBER] ZAFF force field

From: Tabassum Khair Barbhuiya <tabassumkhair.barbhuiya.hdr.qut.edu.au>
Date: Thu, 21 Jan 2021 01:09:11 +0000

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.


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/>
I acknowledge the Turrbal and Yugara, as the First Nations owners of the lands where
QUT now stands. I pay respect to their Elders, lores, customs and creation spirits.
I recognise that these lands have always been places of teaching, research and learning.

This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

AMBER mailing list

(image/jpeg attachment: image003.jpg)

(image/png attachment: image006.png)

Received on Wed Jan 20 2021 - 17:30:02 PST
Custom Search