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Contents

Introduction

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Version and Availability

AutoDock and AutoGrid version 4.2 and 4.3 are available on all LONI x86 Clusters (qb, eric, louie, oliver, painter and poseidon).

Usage

To use AutoDock and AutoGrid, add the soft key (+autodock-4.2-gcc-4.3.2 or +autodock-4.3-gcc-4.3.2) to your .soft file and resoft

Running AutoDock & AutoGrid Calculations

Note that AutoDock and AutoGrid are serial codes, running such calculations on QueenBee or in the workq or checkpt queue will cause core to remain idle for the duration of the run and you will be charged for all cores that are assigned to your jobs.

Sample PBS script to run AutoGrid

 #!/bin/bash
 
 #PBS -A your_allocation
 #PBS -q single
 # single queue is not present on Queen Bee, use workq or checkpt
 #PBS -M your_email
 # Change ppn to 8 if running on Queen Bee
 #PBS -l nodes=1:ppn=1
 #PBS -l walltime=06:00:00
 #PBS -V
 #PBS -o AutoGrid_test.out
 #PBS -e AutoGrid_test.err
 #PBS -N autogridtest
  
 export EXEC=autogrid4
 export INPUT=hsg1.gpf
 export OUTPUT=hsg1.glg
 export WORK_DIR=$PBS_O_WORKDIR
 
 cd $WORK_DIR
 
 $EXEC -p $INPUT -l $OUTPUT

  

Then submit it to run (assuming that the script above is autogrid.pbs):

 qsub autogrid.pbs

Sample PBS script to run AutoDock

 #!/bin/bash
 
 #PBS -A your_allocation
 #PBS -q single
 # single queue is not present on Queen Bee, use workq or checkpt
 #PBS -M your_email
 # Change ppn to 8 if running on Queen Bee
 #PBS -l nodes=1:ppn=1
 #PBS -l walltime=06:00:00
 #PBS -V
 #PBS -o AutoDock_test.out
 #PBS -e AutoDock_test.err
 #PBS -N autogridtest
 
 export EXEC=autodock4 
 export INPUT=ind.dpf
 export OUTPUT=ind.dlg
 export WORK_DIR=$PBS_O_WORKDIR
 
 cd $WORK_DIR
 
 $EXEC -p $INPUT -l $OUTPUT

  

Then submit it to run (assuming that the script above is autodock.pbs), only after the AutoGrid job has successfully completed:

 qsub autodock.pbs

Note: To run a autodock calculations successfully, your autogrid job must complete without errors. If you are comfortable with submit scripts, you can use the following script to submit both the autogrid and autodock job using PBS Job Chains and Dependencies

  #!/bin/bash
 
 FIRST=$(qsub autogrid.pbs)
 echo $FIRST
 SECOND=$(qsub -W depend=afterok:$FIRST autodock.pbs)
 echo $SECOND

References

A wide variety of user resources are available on line.



Users may direct questions to sys-help@loni.org.

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