I have never used expr like you do but you need to decrease the index
by one
i=`expr index $file .`
i=`expr $i - 1`
f1=`expr substr $file 1 $i`
On Fri, 17 Apr 2015 21:15:57 +0530
Pallavi Mohanty <pallavipmohanty.gmail.com> wrote:
> Thanks Hannes and Jason, yes your suggestions did worked but there is
> still an issue. My output is in the form of :output1..crd,
> output1..top, output2..crd ,output2..top and so on.As Hannes had
> suggested below mentioned is the script :
> #! /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
> quit
> _EOF
> done
> -----------------------------------------
> where can be the possible fault?
> Thanking you again!
>
> On Fri, Apr 17, 2015 at 7:12 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Fri, Apr 17, 2015 at 9:31 AM, Hannes Loeffler <
> > Hannes.Loeffler.stfc.ac.uk
> > > wrote:
> >
> > > On Fri, 17 Apr 2015 08:07:17 -0400
> > > Jason Swails <jason.swails.gmail.com> wrote:
> > >
> > > > On Fri, Apr 17, 2015 at 7:17 AM, 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
> > > > >
> > > >
> > > > This doesn't actually work with tleap. stdin must come from a
> > > > tty, otherwise you get an error like this:
> > > >
> > > >
> > > > *** Error: tl_getline(): not interactive, use stdio.
> > > >
> > > > (I've tried this myself before, wishing it would work).
> > >
> > > Yes, because there was no "quit" command. If there is a "quit"
> > > teLeap will never enter the interactive loop and do the isatty()
> > > in gl_init() in getline.c.
> > >
> > > So script should be
> > >
> > > #!/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
> > > quit
> > > _EOF
> > > done
> > >
> >
> > Cool! The "-f -" is essential, it appears (as is the quit, as you
> > mentioned).
> >
> > Thanks!
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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Received on Fri Apr 17 2015 - 09:00:06 PDT
