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 - 11:12:30 CDT

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