You are mixing shell scripting with leap scripting. I guess what you
want is this
#!/bin/sh
for file in output*.pdb; do
i=`expr index $file .`
f1=`expr substr $file 1 $i`
tleap -f - <<_EOF
source leaprc.ff99SB
x = loadpdb $file
saveamberparm x $f1.top $f1.crd
_EOF
done
On Fri, 17 Apr 2015 16:32:00 +0530
Pallavi Mohanty <pallavipmohanty.gmail.com> wrote:
> Dear User,
> I intend to run batch minimization of 500 pdbs hence need to
> generate .top and .crd files. Here is my leap.in file to do the above
> mentioned task : #! /bin/sh
> for file in output*.pdb
> do
> source leaprc.ff99SB
> x = loadpdb $file
> i=`expr index $file .`
> f1=`expr substr $file 1 $i`
> saveamberparm x $f1.top $f1.crd
> done
> But the moment i execute it using "tleap -f leap.in", i end up with an
> error saying
> ----------------------------------------------------
> Substituting map OB -> O2P for OB -> O2P
> Could not open file file: not found
> ERROR: syntax error
>
> ERROR: syntax error
>
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage: saveAmberParm <unit> <topologyfile> <coordfile>
> ERROR: syntax error
> ------------------------------------------------------------------
> PLEASE REPLY WHERE I HAVE GONE WRONG!Thanks for the time you may give
> me!
>
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Received on Fri Apr 17 2015 - 04:30:07 PDT
