On Fri, Apr 17, 2015 at 7:59 AM, Pallavi Mohanty <pallavipmohanty.gmail.com>
wrote:
> Thanks Hannes for your inputs, would you mind to explain me again as i am
> facing the same error!
>
You have to tell us what you've actually done. I suspect what you did was
change the script to Hannes' suggestion and then tried feeding that script
to tleap again. As Hannes said, you are treating LEaP like it properly
understands bash scripting -- it does not.
You have written a bash script and given it to tleap, and it has no idea
what to do with it.
You should have your bash script write tleap scripts and then call tleap.
So something like this:
#!/bin/sh
for file in output*.pdb
do
i=`expr index $file .`
f1=`expr substr $file 1 $i`
cat > tleap.in << EOF
source leaprc.ff99SB
x = loadpdb $file
saveamberparm x $f1.top $f1.crd
EOF
tleap -f tleap.in
done
Then you have to run this script using sh, not tleap (the script calls
tleap). So you can either do this via:
sh script.sh
Or give script.sh execute permissions and run it directly
chmod +x script.sh
./script.sh
(Assuming, of course, that you named your script "script.sh").
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 17 2015 - 05:30:03 PDT
