AMBER Archive (2008)

Subject: Re: AMBER: how to enlarge the TIP3PBOX size

From: Carlos Simmerling (
Date: Wed Sep 24 2008 - 18:01:44 CDT

give us more info- it's hard to say what's going on. the protein
moving out of the box during MD may be normal, and you need to "image"
the trajectory with ptraj. search the archives for plenty of
information and examples. if the box is too small before you run MD.
then you need to increase your buffer size in the solvate command when
you run leap. if you want solvateoct, check the archives or the ptraj
manual, and let us know specific questions. the tutorials can also be
helpful for this.

On Wed, Sep 24, 2008 at 6:56 PM, Qiuting Hong <> wrote:
> Dear amber users,
> I am using TIP3PBOX to solvate ubiquitin. After the explicit water
> simulation, I reimage the water back into the box, but find out part of the
> ubiquitin side chain is out of the water box. I guss the box is too small.
> I am trying to re-run the simulation. But I don't know how to change the
> size of TIP3PBOX. I want to use solvateoct.
> Can somebody help me out?
> Qiuting Hong
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