>From the same coordinate file? That seems unlikely. There's a simple test
you can do to figure out how many frames you have. Each line has 10
coordinates, and each atom requires 3 coordinates. Therefore, each frame
will take natom * 3 /10 lines. Add one line for box information if you have
any. Divide the total number of lines in the coordinate file (you may have
to subtract one if there is a title in the top line) by this number, and
that is how many frames you have. You can find out how many lines are in
your file with "wc -l trajectory".
Good luck!
Jason
On Fri, Jul 2, 2010 at 3:13 AM, c00jsw00 <c00jsw00.nchc.org.tw> wrote:
> Dear Sir,
>
> But, I used the command "trajout out PDB" and I could transfor 500000 sets
> of coordinates.
>
> YT
> On Fri, 2 Jul 2010 01:48:06 -0400, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > On Fri, Jul 2, 2010 at 1:12 AM, c00jsw00 <c00jsw00.nchc.org.tw> wrote:
> >
> >> Dear all,
> >> This is my ptraj input and output ..
> >>
> >> #input
> >> ------------------------------------------------------
> >> trajin afm.x 1 500000 1
> >> reference 2.pdb
> >> rms reference out rms .CA
> >> trajout out
> >>
> >>
> >>
> >> #output
> >> ------------------------------------------------------
> >> PTRAJ: Processing input from "STDIN" ...
> >>
> >> PTRAJ: trajin afm.x 1 500000 1
> >> Checking coordinates: afm.x
> >> FYI ptrajSetupIO(): trajin stop value (500000) is greater than the
> number
> >> of sets read in.
> >> Setting stop to the maximum value (14734)
> >> ..........
> >>
> >>
> >>
> >> >From the output, the ptraj only read 14734 coordunates. How could I do
> >> >to
> >> fix the problem ?
> >>
> >
> > It only read in 14,734 sets of coordinates because that's all there is
> in
> > your coordinate file. If you expect more, then your topology file and
> your
> > mdcrd file are likely incompatible. You can verify this in a
> visualization
> > program.
> >
> > Good luck!
> > Jason
> >
> >
> >>
> >> Thanks
> >>
> >> YT Wang
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Jul 02 2010 - 07:30:08 PDT
