First, you're telling ptraj to process frames one to ten thousand,
skipping every 50 million, so only frame 1 will ever be processed. Did
you mean 'trajin 1 50000000 10000'?
Second, have you tried to process the trajectory file with cpptraj?
Does it give the same error?
-Dan
On Wed, Jun 13, 2012 at 2:01 PM, vishal kumar Jaiswal
<vishal3990.gmail.com> wrote:
> I performed a simulation of 100 ns on a AC dinucleotide in water. this has
> resulted in a large mdcrd file of 34 gigabytes.
>
> I am trying to use ptraj to process this (to strip out the wat and cut it
> to more manageable size but ptraj is unable to read it.
>
> I get the following error
> PTRAJ: trajin AC_wat_md3.mdcrd 1 10000 50000000
> Checking coordinates: AC_wat_md3.mdcrd
>
> Could not open file (AC_wat_md3.mdcrd) with mode (r)
> WARNING in checkCoordinates(): Could not open file (AC_wat_md3.mdcrd)
> WARNING in ptrajSetupIO(): trajin AC_wat_md3.mdcrd, cannot open file...
>
> I am able to load the mdcrd file in vmd and see the trajectory, so
> the file is fine.
>
> Can you suggest me how to process this crd file
> ( are there any other methods to convert it to binpos etc ) or any other
> way......
>
> thank You
>
> Vishal Kumar Jaiswal
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--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jun 13 2012 - 12:00:03 PDT
