AMBER Archive (2008)

Subject: Re: AMBER: Tutorial B3- Section6

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Apr 11 2008 - 05:26:28 CDT

are you inside ptraj when you type trajin? it is a ptraj command, not a bash
shell command.

On Thu, Apr 10, 2008 at 7:50 PM, Chih-Ying Lin <chihying_at_usc.edu> wrote:

>
>
> 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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