Re: [AMBER] sleap log

From: case <>
Date: Thu, 3 Jun 2010 16:06:33 -0400

On Thu, Jun 03, 2010, Omair A. Khan wrote:
> Update on my post: I opened the PDB file that was generated with water
> residues in PyMol and it definitely does NOT give me a box. The water
> is strangely dispersed, sort of like it "sneezed." Is there an error
> in my code?

Have you run dynamics? If so, it is likely to be an imaging problem -see the
image command in ptraj.

If your box looks funny right after tleap, study the first tutorial: this
illustrates solvation with a water box, and shows you what the output should
look like.


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Received on Thu Jun 03 2010 - 13:30:03 PDT
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