AMBER Archive (2008)

Subject: Re: AMBER: help...ptraj does not output bounding box info

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 03 2008 - 12:53:33 CDT

its more than just that section- here is a link to the file format for
the prmtop files.
ifbox is one of the flags at the start of the file. I'm not sure if
you can just change it and add the box info, might be worth trying.
I would not do that for a real simulation, but for analysis it might work.
http://www.ambermd.org/formats.html

On Wed, Sep 3, 2008 at 1:26 PM, Jose Borreguero <borreguero_at_gmail.com> wrote:
> Dear Carlos and Bill,
>
> Thanks for your comments. I finally saw the light :)
> I have two "file.top" files, one for the solvated system (solvateBox), the
> other for the unsolvated system. Only the solvated "file.top" does have a
> BOX_DIMENSIONS flag. I could not find the "ifbox" flag that you mentioned,
> though.
> I only have one "file.crd" file which corresponds to an equilibrium
> trajectory of the solvated system but with the solvent and ions stripped to
> save disk space.
> For starters, I just copied/pasted the BOX_DIMENSIONS info from the solvated
> "file.top" to the unsolvated "file.top". It didn't solved the problem
> What worked was building the unsolvated system from scratch with tleap,
> explicitly setting the box property:
> tleap
>> source source leaprc.ff98
>> unit=loadPdb file.pdb
>> dims={50.507 47.724 51.056}
>> set unit box dims
>> saveAmberParm unit file.top another_junk.crd
>>quit
> Now I can use this file.top along with file.crd in ptraj. The bounding box
> is saved now in junk.crd
> Many thanks for your help!
> -Jose
>
> On Wed, Sep 3, 2008 at 12:23 PM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
>>
>> I think if ifbox is not 1 in the prmtop, ptraj won't write the box info.
>> you might try setting a box in leap without adding solvent (perhaps
>> solvatebox but use a small buffer and large closeness?) and using that
>> for ptraj.
>> if there is no periodic box defined, I'm wondering how the box size
>> got into the crd file in the first place- sander doesn't do that I
>> think.
>> carlos
>>
>>
>> On Wed, Sep 3, 2008 at 12:12 PM, Jose Borreguero <borreguero_at_gmail.com>
>> wrote:
>> > No, the bounding box info is in "file.crd", one for each frame within
>> > "file.crd".
>> > Just to try, I explicitly included a box command:
>> >> trajin file.crd
>> >> box 50.507 47.724 51.056
>> >> trajout junk.crd
>> >> go
>> > unfortunately, the box was not written into "junk.crd"
>> >
>> >
>> > On Wed, Sep 3, 2008 at 11:41 AM, Carlos Simmerling
>> > <carlos.simmerling_at_gmail.com> wrote:
>> >>
>> >> does file.top have a periodic box defined?
>> >>
>> >> On Wed, Sep 3, 2008 at 11:39 AM, Jose Borreguero <borreguero_at_gmail.com>
>> >> wrote:
>> >> > Hi,
>> >> > The trajout command does not output the bounding box info for a given
>> >> > input
>> >> > trajectory. Here's a little example: assuming "file.crd" is a
>> >> > trajectory
>> >> > containing the bounding box info for each frame:
>> >> > ptraj file.top
>> >> >> trajin file.crd
>> >> >> trajout junk.crd
>> >> >>go
>> >> > File "junk.crd" is identical to "file.crd" except the bounding box
>> >> > lines
>> >> > are
>> >> > missing. This is true also for other output formats like "trajout
>> >> > junk.crd
>> >> > netcdf".
>> >> > Is there any way to keep these lines ?
>> >> > Best regards,
>> >> > --
>> >> > Jose M. Borreguero
>> >> > Postdoctoral Associate
>> >> > Oak Ridge National Laboratory
>> >> > P.O. Box 2008, M.S. 6164
>> >> > Oak Ridge, TN 37831
>> >> > phone: 865-241-3071 fax: 865-576-5491
>> >> > Email: borreguerojm_at_ornl.gov
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> ===================================================================
>> >> Carlos L. Simmerling, Ph.D.
>> >> Associate Professor Phone: (631) 632-1336
>> >> Center for Structural Biology Fax: (631) 632-1555
>> >> CMM Bldg, Room G80
>> >> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>> >> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> >> ===================================================================
>> >> -----------------------------------------------------------------------
>> >> The AMBER Mail Reflector
>> >> To post, send mail to amber_at_scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> >> to majordomo_at_scripps.edu
>> >
>> >
>> >
>> > --
>> > Dr. Jose M. Borreguero
>> > Postdoctoral Associate
>> > Oak Ridge National Laboratory
>> > P.O. Box 2008, M.S. 6164
>> > Oak Ridge, TN 37831
>> > phone: 865-241-3071 fax: 865-576-5491
>> > Email: borreguerojm_at_ornl.gov
>> >
>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Associate Professor Phone: (631) 632-1336
>> Center for Structural Biology Fax: (631) 632-1555
>> CMM Bldg, Room G80
>> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>> ===================================================================
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>
>
>
> --
> Dr. Jose M. Borreguero
> Postdoctoral Associate
> Oak Ridge National Laboratory
> P.O. Box 2008, M.S. 6164
> Oak Ridge, TN 37831
> phone: 865-241-3071 fax: 865-576-5491
> Email: borreguerojm_at_ornl.gov
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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