Re: [AMBER] does CHECKOVERLAP check image cell?

From: kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
Date: Thu, 27 Oct 2011 10:33:41 +0900

Dear Prof. Cheatham,

Thank you for kind support.
I will try that.

Yours sincerely,

                      IK




-----Original Message-----
From: Thomas Cheatham III [mailto:tec3.utah.edu]
Sent: Thursday, October 27, 2011 5:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] does CHECKOVERLAP check image cell?


> I am now trying to identify small ligand cluster.
>
> Here I use "checkoverlap" in ptraj modules.
...
> I am feeling that "checkoverlap" checks not only real cell but also image
> cell.

Yes, by default this does check image cells since in fact images could
overlap... To avoid this, add the "noimage" keyword.

--tec3

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Received on Wed Oct 26 2011 - 19:00:03 PDT
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