On Wed, Apr 09, 2008, Chih-Ying Lin wrote:
>
>
> After type the two commands,
> $AMBERHOME/exe/ptraj TC5b.prmtop < measure_rmsd.trajin > measure_rmsd.out
> $AMBERHOME/exe/ptraj TC5b.prmtop < extract_frame9_2455.trajin > extract_frame9_2455.out
>
> I got the two following files and they are EMPTY.
> extract_frame9_2455.out
> measure_rmsd.out
>
>
> $AMBERHOME/exe/ptraj TC5b.prmtop <mdcrd_to_binpos.ptraj >mdcrd_to_binpos.out
> Also, I got a EMPTY mdcrd_to_binpos.out
It's pretty clear that ptraj is not working for you. Try running the commands
without the "<" and ">" redirections. Make sure that the input files are there.
Do the ptraj test cases pass? Look especially at the tests in
amber9/test/ptraj_rms. Assuming things pass, try to figure out what you are
doing that is different from the tests.
...dac
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Received on Fri Apr 18 2008 - 21:18:15 PDT
