Re: [AMBER] water box corrupted by minimization

From: Nagar, Hemant <>
Date: Fri, 5 Nov 2021 14:26:33 +0000

Try with this .trajin script to extract out your frames.
trajin " (.nc file from production run)"
center :a -b mass origin "[a(first residue number)-b(last residue number), # residue number in your file]"
image origin center
trajout prod_run_frames_COM.pdb ( output file name)

-----Original Message-----
From: David A Case <>
Sent: Friday, November 5, 2021 9:30 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] water box corrupted by minimization

On Thu, Nov 04, 2021, Michael Shokhen wrote:
>The periodic water box is corrupted by minimization procedure.
>See scripts and figures below.
>I need your advice how to resolve the problem.

Here is a similar report:;;sdata=e2UEKSS5RWpRMo1T6fDjzezSfLyTDN%2FPS6hxHelZB6E%3D&amp;reserved=0

Tom lists some ideas for exploring what is going on, and suspects that it is "just" a visualization artifact. It's not clear that the original poster last month ever supplied any files that would allow one to reproduce the problem, so if you could do that, it would probably help.


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Received on Fri Nov 05 2021 - 07:30:02 PDT
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