Tommy.
on a different note. Can you post your mdin here? Depending on the type
of run you are trying to do, running it for only 200 ps and rstarting
could cause some trouble.
adrian
On 6/19/12 3:40 AM, Tommy Yap wrote:
> 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
>>>>
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>>>>
>>>
>>>
>>>
>>
>>
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>>
>
>
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Jun 19 2012 - 06:30:02 PDT
