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
Cheers,
Hannes.
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Received on Fri Apr 17 2015 - 07:00:02 PDT
