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PostPosted: Fri Mar 08, 2013 1:50 am 
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Millimolar User
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Joined: Mon Feb 04, 2013 1:55 am
Posts: 9
Hello,

This a feature request unless it already exists (and someone can point me to it)...

During in-silico HTS runs, we are seeing most of our entries taking between 0-5 minutes to complete with Vina at default exhaustiveness 8. However, a very small amount of entries in our database are taking >15 hours according to `top`. I have seen this happen before and it has not bothered me, but these compounds are starting to bottleneck my runs, and I are unsure whether the time spent on these very few compounds is 'worth the time' (ie the chance of any of them being a good lead).

I was wondering if there was a flag that allowed a maximum time permitted for vina to attempt to dock before it simply terminated, so we could set a 'timeout' for computationally troublesome compounds.

Otherwise I may have to implement a daemon that monitors vina processes for time and forcibly kills the process after a certain length of time.

Kind regards,
Sebastian


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PostPosted: Sat Jun 15, 2013 1:31 am 
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Joined: Thu Apr 16, 2009 7:31 pm
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You've probably already come up with your own solution by now, but FWIW....

If you're doing your screen by launching docking processes from within a shell script - e.g.

#!/bin/bash
for f in *dpf
do
echo $f
autodock4 -p $f -l `basename $f .dpf`.dlg &
wait
done


you can add a line of perl code before your docking command that will set a time limit on that process (60sec in this example)


#!/bin/bash
for f in *dpf
do
echo $f
perl -e 'alarm shift @ARGV; exec @ARGV' 60 autodock4 -p $f -l `basename $f .dpf`.dlg &
wait
done



credit where it's due: http://stackoverflow.com/questions/6015 ... nt-of-time?


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PostPosted: Sun Jun 16, 2013 1:41 am 
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Joined: Mon Feb 04, 2013 1:55 am
Posts: 9
thanks, I'll keep this solution in mind.

Cheers
Sebastian


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