Re: [AMBER] Imaging everything inside an octahedral box

From: Daniel Roe <>
Date: Mon, 18 Jul 2011 09:52:14 -0400


Without knowing what you have already tried I can only guess as to
what might help, but try something like this:

center :1-X
image origin center familiar

where X is the last residue of your protein. If you absolutely need
every single atom inside the box boundaries, you could add the
'byatom' keyword, but be aware this can split up molecules (which
would be a real problem if for example you plan on using the resulting
structures for
MD or energy analysis later on).


On Sun, Jul 17, 2011 at 10:57 AM, Daniel Kuroda <> wrote:
> Hi all,
> I have been trying unsuccessfully to wrap a protein inside an
> octahedral box and the reason is because to do so ptraj has to cut the
> protein which is not suppose to happen. Now my question is plain
> simple: is there any way to wrap everything inside an octahedral box
> with ptraj? And when I say everything, I mean everything (protein,
> water, etc.) even if this demands to split some molecules.
> Thanks
> Daniel
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Received on Mon Jul 18 2011 - 07:00:03 PDT
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