I just tried to compress the crd file . Now the ptraj seems to handle it
somewhat but not completely. this is what I get :
PTRAJ: trajin AC_wat_md3.mdcrd.tar.gz 1 10000 50000000
Checking coordinates: AC_wat_md3.mdcrd.tar.gz
WARNING in ptraj(): Offset is so large that only 1 set
will be processed...
PTRAJ: trajout AC_wat_md3.bps binpos box
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 1 frames.
Summary of I/O and actions follows:
Any ideas ..........???
On Wed, Jun 13, 2012 at 8:01 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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Received on Wed Jun 13 2012 - 12:00:02 PDT
