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 - 13:28:02 CDT

Setting IFBOX to 1 and adding the box info is not enough. There are two
other flags that must be set, too:
%FLAG *SOLVENT_POINTERS*
%FORMAT(3I8)
      54 2 3
%FLAG *ATOMS_PER_MOLECULE*
%FORMAT(10I8)
     788 1
After including this, the modified "file.top" becomes identical to the
"file.top" generated with tleap.

On Wed, Sep 3, 2008 at 1:53 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> 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
> ===================================================================
> -----------------------------------------------------------------------
> 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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