I think you have to remove the spaces before _EOF in the second last line. For testing purposes replace "tleap -f -" with "cat".
________________________________________
From: Pallavi Mohanty [pallavipmohanty.gmail.com]
Sent: 17 April 2015 12:59
To: AMBER Mailing List
Subject: Re: [AMBER] Batch leap error!
Thanks Hannes for your inputs, would you mind to explain me again as i am
facing the same error!
On Fri, Apr 17, 2015 at 4:47 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> 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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>
--
Regards,
Pallavi Mohanty
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Received on Fri Apr 17 2015 - 06:00:05 PDT
