Re: [AMBER] Defining the box dimensions while making the top and crd files

From: David A Case <>
Date: Fri, 26 Jun 2015 21:59:55 -0400

On Fri, Jun 26, 2015, Iqbal, Muhammad Sajid wrote:
> *set mypdb box {300.05 300.0 300.08}*
> However, I could not get the right values after running the pre-MD
> minimization step. After performing minimization step, my pdb file
> coordinates are look like this which is quite different.

I'm lost: can you explain what you mean by "could not get the right values"?
(What values? What happened?)

It's also unclear what you mean by "my pdb file coordinates ...look like
this". (Look like what? If you are visualizing things, did you use the
"autoimage" command in cpptraj first?)


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Received on Fri Jun 26 2015 - 19:30:03 PDT
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