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
>>
>
>
>
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Received on Tue Jun 19 2012 - 00:30:03 PDT
