AMBER Archive (2008)

Subject: Re: AMBER: Tutorial B3- Section6

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu Apr 10 2008 - 18:50:14 CDT

Hi
otherwise, i type
trajin xxx.mdcrd

it shows...
-bash: trajin: command not found

any idea for this??

thanks
Lin

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, April 9, 2008 6:49 pm
Subject: Re: AMBER: Tutorial B3- Section6
To: amber_at_scripps.edu

> 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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