Hi Fernando,
It's not 100% clear to me what you are asking. Just to be clear, is
there a problem with autoimage in cpptraj?
It sounds to me like what you have are two subunits oriented in your
rectangular box such that the axis on which you want to separate them
is short, and you would like to re-orient the box so that they can be
separated along the long axis - is that correct? If so I don't think
there is an easy way to do it. I'm kinda just reaching here, but you
could try something like maybe aligning the non-solvated system along
its principal axis (using the 'principal command'), printing it out as
a PDB, loading it into leap, then adding a box with the solvatebox
command, manually specifying the dimensions (e.g. 'solvatebox m
TIP3PBOX {<xsize> <ysize> <zsize>}'). Again, I'm not sure this is even
what you want, but hopefully some of this was helpful.
-Dan
On Wed, Sep 12, 2012 at 7:11 AM, Fernando Martín García
<fmgarcia.cbm.uam.es> wrote:
> Dear Amber users,
>
> Recently, we have updated ambertools12 in order to use autoimage
> option. Command works fine but we have a doubt: we see water box move
> respect to anchor mask, but, is there any possibility to say cpptraj to
> make a rotation of the box respect anchor?. We are performing a MTMD and
> we want separate two subunits, but we have a rectangular box, so what we
> wanted was to orient our box to the separation direction. I don't if it
> could be possible or not.
>
> Thanks,
>
> Fernando
> --
> ==============================================
> Fernando Martín García
> Molecular Modelling Group - Lab 312.1
> Molecular Biology Center "Severo Ochoa"
> C/ NICOLáS CABRERA, 1.
> UAM University. Cantoblanco, 28049 Madrid. Spain.
> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> Web: http://fertoledo.wordpress.com/
> ==============================================
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Sep 12 2012 - 08:30:02 PDT
