Thanks...i will change the script and try running to see if it works.
Thanks again.
On Tue, Jun 19, 2012 at 3:05 PM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Hi Tommy,
>
> there is a space missing between "." and "CURRENT" (last line of your
> WHILE loop). This space is required, however, and therefore you're
> getting the error ".CURRENT: Command not found", while your first
> numerical assignment works well. Additionally, the CURRENT-variable
> lacks its "$" prefix:
>
> .CURRENT = CURRENT + 1
> =>
> . CURRENT = $CURRENT + 1
>
> So, your error has nothing to do with Amber but with shell scripting.
>
> Regards,
>
> Anselm
>
>
> Am 19.06.2012 06:49, schrieb Tommy Yap:
> > This is how my log file look like:
> >
> > Starting script at:Mon Jun 11 10:15:44 MYT 2012
> >>
> >> Job 3 started at:Mon Jun 11 10:15:44 MYT 2012
> >> md3.mdcrd: 60.8% -- replaced with md3.mdcrd.gz
> >> Job 3 finished at:Wed Jun 13 00:34:51 MYT 2012
> >> .CURRENT: Command not found.
> >> Job 3 started at:Wed Jun 13 00:34:51 MYT 2012
> >> gzip: md3.mdcrd.gz already exists; do you wish to overwrite (y or n)?
> >>
> >
> > At the end of MD, i only get one file when 5 files of 200ps is expected.
> > Can you help? Thanks
> >
> > On Tue, Jun 19, 2012 at 11:58 AM, Niel Henriksen<niel.henriksen.utah.edu
> >wrote:
> >
> >>
> >> There are many possibilities. If you could post any
> >> error messages from the output files that would
> >> help us determine the problem.
> >>
> >> --Niel
> >> ________________________________________
> >> From: Tommy Yap [tommyyap87.gmail.com]
> >> Sent: Monday, June 18, 2012 9:06 PM
> >> To: AMBER Mailing List
> >> Subject: [AMBER] Script error to restart MD automatically
> >>
> >> Dear all,
> >>
> >> I used this script to restart my MD runs automatically and it worked
> well
> >> in AMBER8. But now I am using AMBER11 and the script does not seem to
> work
> >> anymore. Can anyone help to check if there is any problem with the
> script?
> >>
> >> My script looks like this:
> >>
> >> #!/bin/csh
> >>> set AMBERHOME="/usr/local/amber11"
> >>> set START=3
> >>> set END=7
> >>> set CURRENT=$START
> >>> set INPUT=0
> >>>
> >>> echo -n "Starting script at:"
> >>> date
> >>> echo ""
> >>>
> >>> while ($CURRENT<= $END)
> >>> echo -n "Job $CURRENT started at:"
> >>> date
> >>> . INPUT = $CURRENT - 1
> >>> $AMBERHOME/exe/sander -O -i md_short.in -o md$CURRENT.out -p
> >>> alasub_wat.prmtop -c md$INPUT.rst -r md$CURRENT.rst -x md$CURRENT.mdcrd
> >>> gzip -9 -v md$CURRENT.mdcrd
> >>> echo -n "Job $CURRENT finished at:"
> >>> date
> >>> .CURRENT = CURRENT + 1
> >>> end
> >>> echo "YES!! JOB DONE!!"
> >>>
> >>
> >> Please help. Thanks
> >>
> >> -TOMMY-
> >> --
> >> Regards,
> >> Tommy Yap
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Tommy Yap
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Received on Tue Jun 19 2012 - 01:00:02 PDT
