Re: AMBER: Protein rotating out of box

From: Lars SkjŠrven <>
Date: Wed, 2 Apr 2008 21:17:23 +0200

thanks again for feedback.

Both vmd and xleap is used for visualization. tLeap adds a total of
40k waters, which is ~50k less than when i solvate with 'solvatebox
5┼'. Thus, I doubt visualization is the reason for this.

Amber9 with the newest bugfixes is used. I've tried this on three
independent machines (SGI altix, and two linux boxes). Portland group
compilers has not been used on any of the installations.

When I reduce the size of the same protein by 50%, it solvates as expected.


On Wed, Apr 2, 2008 at 7:35 PM, Qiang Li <> wrote:
> Hi,
> I meet the same problem too. I was following the tutorial on AMBER website,
> and I never manage to put the whole DNA into the box. I am using amber 8,
> Portland Group compiler, and AMD opteron. David A. Case just told me that
> the PGC should be the reason. Are you using PGC too?
> --Qiuting Hong
> ----- Original Message ----
> From: Thomas Cheatham III <>
> To:
> Sent: Wednesday, April 2, 2008 9:54:46 AM
> Subject: Re: AMBER: Protein rotating out of box
> > Thanks for your comments. I guess the solvateoct is the way to go
> > here. However, after I solvate using the command:
> > 'solvateoct mol TIP3PBOX 15.0 0.78' parts of the solute is outside the
> > box. Hmm.. Does not the buffer argument, in this case 15.0┼, specify
> > the distance between the wall of the box and the closest atom? Or is
> > it the distance to the walls in the cubic box, and then it shawes off
> > the corners no matter if the solute is in the way? I have to make the
> > buffer as high as 33┼ to get the solute entirely inside the box.
> --------------------------
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mvh Lars SkjŠrven
Institutt for Biomedisin
Universitetet i Bergen
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Received on Fri Apr 18 2008 - 21:16:15 PDT
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