Hi Dan,
That's exactly the problem. And no, there isn't any problem with
ccptraj according to this.
Yes, we have been made this option you suggest, but we wanted to skip
these steps, avoiding the equilibration of the box again. I know it's
difficult what I propose, but only to know if cpptraj had this option.
Thanks for the suggest.
Fer
On Wed, 12 Sep 2012 09:14:36 -0600, Daniel Roe wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
==============================================
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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Received on Wed Sep 12 2012 - 23:30:04 PDT
