Re: [AMBER] Equilibration

From: Lizelle Lubbe <>
Date: Thu, 23 Nov 2017 07:23:36 +0000

Dear Sara,

I have simulating the same protein and experienced some issues in the past regarding the catalytic zinc ion. Did you derive your own metal coordination site parameters for these simulations?

Kind regards

Lizelle Lubbe

PhD (Chemical Biology) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
South Africa

From: <>
Sent: 23 November 2017 08:30:54 AM
Subject: Re: [AMBER] Equilibration

Dear Bill,

I checked the RMS fittings and observed that there was a prominent
fluctuation in the RMSD of the terminal residues (19 residues). I have
attached images of the protein showing the terminal residue and the RMSD
fluctuation. Shall i continue with the production or do I have to
cap/remove the terminal and start over.

Best REgards,
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Received on Wed Nov 22 2017 - 23:30:02 PST
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