> 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.
Hopefully we can get this fixed in the next version of FEW so this is no longer necessary.
Thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 23 2015 - 08:00:04 PDT
