[AMBER] MCPB.py ZINC Mediated interactions parameterization

From: Rana Rehan Khalid <ray.binm.gmail.com>
Date: Mon, 15 Mar 2021 17:56:17 -0400

Dear Amber User


I am working on ZN mediated interactions system that are as follow

ZN ion interacts with ---------2 aspartic acids,
ZN ----------O atom of Ligand
ZN ---------- with histidine.
ZN ------------F atom of ligand

I have prepared the smaller and larger model by using
 MCPB.py -i 1OKL.in -s 1
This generates a smaller and larger model, I am confused that why the
smaller model showed a bond between ASP and histidine rather than ZN
mediation. Please guide me in this regard. I am attaching the published
interaction system image and my MCPB generated small system images.

Thank you so much.

Best
Rehan


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1.png
(image/png attachment: 1.png)

system.png
(image/png attachment: system.png)

small.pdb.png
(image/png attachment: small.pdb.png)

Received on Mon Mar 15 2021 - 15:00:02 PDT
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