On Mon, 23 Mar 2015 10:41:10 -0400
Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Mar 23, 2015, at 7:57 AM, Michael Shokhen
> > <michael.shokhen.biu.ac.il> wrote:
> >
> > Hi Jason,
> >
> > I have read your discussion with Michele regarding my
> > error report in A24 Amber tutorial.
> >
> > Let me remind you the subject of error when doing A24 tutorial:
> >
> > ➜ ~ cd $FEW
> > ➜ ~FEW pwd
> > /home/shokhen/amber14/AmberTools/src/FEW
> > ➜ ~FEW perl $FEW/FEW.pl
> > MMPBSA /home/shokhen/tutorial/cfiles/leap_am1
> >
> > #####################################################
> > # #
> > # FEW #
> > # Free Energy Workflow #
> > # #
> > #####################################################
> >
> >
> > Checking input parameters and files.
> > sh: 1: Syntax error: Bad fd number
> > Cannot open file log.txt for reading.
> >
> > You asked:
> >
> >> I couldn't tell from looking at the FEW directory where this
> >> script is -- do you know which script this is?
> >
> > I suggest that the problem file is FEW.pl
> > that locates in a standard AmberTools 14 path:
> > /home/shokhen/amber14/AmberTools/src/FEW/FEW.pl
>
> I meant the shell script that gives the error
>
> sh: 1: Syntax error: Bad fd number
>
> But it turns out to be a command launched from within FEW.pl
> somewhere. Ack... I see no way to get around this without
> changing /bin/sh to point to bash instead of dash.
I suspect it's line 1100 in ./libs/check_input.pm (exec to antechamber).
Apparently dash doesn't like the >& redirection (for both stdout and
stderr).
Cheers,
Hannes.
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Received on Mon Mar 23 2015 - 08:00:05 PDT
