AMBER Archive (2004)

Subject: Re: AMBER: protein is out of the water box

From: David A. Case (case_at_scripps.edu)
Date: Wed May 26 2004 - 11:17:00 CDT

On Tue, May 25, 2004, Feng, Hanqiao (NIH/NCI) wrote:

> I am a new user of AMBER. I tried to follow one of the AMBER Tutorials "
> loop dynamics of the HIV-1 integrase core domain(from Matt Lee)" to prepare
> the sample for minimization. The program just works fine. The only thing I
> changed is to switch "solvateBox mol WATBOX216 10" to "solvateBox mol
> TIP3PBOX 10" because the first didn't work. But finally I used ambpdb to
> convert the parm and crd files to pdb file, I found the protein is out of
> the water box, they are totally separated. Could you please tell me what's
> wrong.
>

If this happens _after_ an MD run, your probably need to image your
coordinates. See the "image" command in ptraj.

If the situation you describe is found in the file you created in LEaP, we
would need more details.

...dac
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