Re: [AMBER-Developers] ptraj issue

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 29 Mar 2010 18:02:25 -0400

Hi Jason,

Good catch - the checkCoordinates() routine was not correctly testing for
box coords when the trajectory is only one frame long. This patch should fix
it - apply in the ptraj source directory (full details are at the top of the
patch file). Let me know if this fixes the problem.

-Dan

On Mon, Mar 29, 2010 at 4:57 PM, Jason Swails <jason.swails.gmail.com>wrote:

> Hello,
>
> I've encountered an issue with ptraj that is probably rarely used but
> is quite easy to reproduce:
>
> trajin mdcrd 1 1 1
>
> trajout frame.mdcrd
>
> This returns the following:
>
> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: _MMPBSA_complex.mdcrd
> If this is not a compressed file then there is a problem
>
> WARNING in safe_close(): Attempting to close a NULL FILE and buffer!
>
> It appears as though ptraj is having some difficulties with
> single-frame trajectory files.
>
> All the best,
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>



-- 
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ   08854



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Received on Mon Mar 29 2010 - 15:30:02 PDT
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