AMBER Archive (2008)

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

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Wed Sep 03 2008 - 12:26:57 CDT

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

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