Hi,
Ptraj can potentially have problems with very large files. A bugfix
has been released that deals with some of these issues.
Have you applied all of the bugfixes? Also, what is the size of the
trajectory file? Thanks!
-Dan
On Fri, Apr 8, 2011 at 11:48 AM, Lui <ltl.cs.nott.ac.uk> wrote:
> Dear all,
>
> I'm trying to use PTRAJ to calculate the distance between the different
> residues.
> The input file is simply:/
>
> trajin data.trj 1 4535 1
> distance d1-2 :1 :2 out dis1.5.list/
>
> My data file is in the form of AMBER trajectory (also called AMBER
> coordinate in VMD), uncompressed.
> When I run PTRAJ, i get the following error
>
> /checkCoordinates(): Could not predict number of frames for AMBER
> trajectory file: data.trj
> If this is not a compressed file then there is a problem/
>
> The last line of the ptraj.out file is
>
> /Processing AMBER trajectory file data.trj/
>
> The trajectory file can be opened with VMD and the visual output looks
> perfectly normal.
>
> I have used the same script and method for another trajectory file, and
> it worked without any problem.
>
> I'm using AmberTools 1.4.
>
> Any suggestions?
>
> Thank you.
>
> Regards,
> Lui
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 08 2011 - 09:30:02 PDT
