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 - 11:23:28 CDT

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
>> ===================================================================
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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
> 

-- 
===================================================================
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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