The Molecular Graphics Laboratory Forum

Hello everybody,

does anybody's using vina on a celuster with SGE ? If yes could you eventually supply jobs submission files ?

Thanks

nicolas

HELLO, i solved my problem and then reply to my own post ....
Here follows an example script to run VINA on a ROCKS cluster with SGE and qsub as a queue sheduler.

Hope it will help.

Nicolas

#!/bin/csh

rm -rf ./DOCKINGS
mkdir ./DOCKINGS

foreach s (`ls ./STRUCTURES/*.pdbqt`)
set struct = `basename $s .pdbqt`
echo Processing Structure $struct

mkdir -p ./DOCKINGS/$struct

foreach f (`ls ./LIGANDS/*.pdbqt`)
set b = `basename $f .pdbqt`
echo Processing ligand $b
mkdir -p ./DOCKINGS/$struct/$b

echo "/mnt/pvfs2/VINA/vina --cpu 1 --exhaustiveness 20 --num_modes 20 --energy_range 10 --receptor $s --ligand $f --center_x 124.2 --center_y 111.5 --center_z 28.4 --size_x 25 --size_y 25 --size_z 25 --out ./DOCKINGS/${struct}
/${b}/solutions.pdbqt --log ./DOCKINGS/${struct}/${b}/log.txt " > job.sh

qsub -q all.q -cwd -o output.std -e output.err -m esa -M root job.sh

sleep 0.1

rm -f job.sh

end

end

Dear nicolas,

Actually, I used some kind of cluster that using Sun Grid Engine too.
I would like to try your script
can you give me some explanation of using this script?
such us, where should I put the receptor etc

Thanks

Muhammad H Hilman

Is there any way to reserve a single node for a vina job in SGE. I have tried to do a "qsub -l slots=2 Job.sge" style submission and it failed saying you need to use parallel environment. Is there another way to have SGE allocate a single node to a single job? This would allow multiple cores to work on a docking. Although this would not be helpful, time wise, for large numbers of ligands but small batches could run faster.

_________________
TJ Mustard
mustardt(at)onid(dot)orst(dot)edu

Not sure about SGE specifically, but the qsub I use has an option for requesting the number of CPUs (cores) per node.
Check the manual.

_________________
Please do not email or PM me with questions. Vina.scripps.edu/questions.html explains where to find help.

Thank you very much for your script. It was generous of you.

I am anxious to begin testing on my own and will report back.