AMBER Archive (2008)

Subject: Re: AMBER: Tutorial B3- Section6

From: David A. Case (
Date: Wed Apr 09 2008 - 20:46:16 CDT

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.


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