autodock
Table of Content
Versions and Availability
About the Software
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.
- Homepage: http://autodock.scripps.edu/
Usage
Please be aware that AutoDock and AutoGrid are serial (non-parallel) codes. It should be run
in a single
queue which will use one processor core. Running in any other queue
will cause cores to be idle, but the job will be charged for all cores.
AutoGrid is required to be executed prior to Autodock
usage: AutoGrid4 -p parameter_filename -l log_filename -d (increment debug level) -h (display this message) --version (Print audogrid version) usage: AutoDock4 -p parameter_filename -l log_filename -k (Keep original residue numbers) -i (Ignore header-checking) -t (Parse PDBQT file for torsions,then stop.) -d (Increment debug level) -C (Print copyright notice) --version (Print autodock version) --help (Display this message)
To successfully run a autodock simulation, first run autogrid simulation to generate a map around receptor atoms around which potentials are to be computed.
▶ Open Example?
#!/bin/bash #PBS -A your_allocation #PBS -q single # Note: a single queue is not present on Queen Bee, # use workq or checkpt, but you will be charged for all cores. #PBS -M your_email # Change ppn to match cluster (4, 8 or 16) if no single queue. #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
Submit your script using qsub
.
▶ QSub FAQ?
Portable Batch System: qsub
qsub
All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.
Usage
$ qsub job_script
Where job_script is the name of the file containing the script.
PBS Directives
PBS directives take the form:
#PBS -X value
Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.
Example Job Script
#!/bin/bash # # Use "workq" as the job queue, and specify the allocation code. # #PBS -q workq #PBS -A your_allocation_code # # Assuming you want to run 16 processes, and each node supports 4 processes, # you need to ask for a total of 4 nodes. The number of processes per node # will vary from machine to machine, so double-check that your have the right # values before submitting the job. # #PBS -l nodes=4:ppn=4 # # Set the maximum wall-clock time. In this case, 10 minutes. # #PBS -l walltime=00:10:00 # # Specify the name of a file which will receive all standard output, # and merge standard error with standard output. # #PBS -o /scratch/myName/parallel/output #PBS -j oe # # Give the job a name so it can be easily tracked with qstat. # #PBS -N MyParJob # # That is it for PBS instructions. The rest of the file is a shell script. # # PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS: # # 1. Copy the necessary files from your home directory to your scratch directory. # 2. Execute in your scratch directory. # 3. Copy any necessary files back to your home directory. # Let's mark the time things get started. date # Set some handy environment variables. export HOME_DIR=/home/$USER/parallel export WORK_DIR=/scratch/myName/parallel # Set a variable that will be used to tell MPI how many processes will be run. # This makes sure MPI gets the same information provided to PBS above. export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro". cp $HOME_DIR/hydro $WORK_DIR cd $WORK_DIR mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro # Mark the time processing ends. date # And we're out'a here! exit 0
If you have successfully run the autogrid simulation to completion, you can run the autodock simulation
▶ Open Example?
#!/bin/bash #PBS -A your_allocation #PBS -q single # Note: a single queue is not present on Queen Bee, # use workq or checkpt, but you will be charged for all cores. #PBS -M your_email # Change ppn to match cluster (4, 8 or 16) if no single queue. #PBS -l nodes=1:ppn=1 #PBS -l walltime=06:00:00 #PBS -V #PBS -o AutoDock_test.out #PBS -e AutoDock_test.err #PBS -N autogridtest export EXEC=autodock4 export INPUT=ind.dpf export OUTPUT=ind.dlg export WORK_DIR=$PBS_O_WORKDIR cd $WORK_DIR $EXEC -p $INPUT -l $OUTPUT
Submit your script using qsub
.
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
▶ PBS Job Chains and Dependencies FAQ?
PBS Job Chains
Quite often, a single simulation requires multiple long runs which must be processed in sequence. One method for creating a sequence of batch jobs is to execute the qsub to submit its successor. We strongly discourage recursive, or "self-submitting," scripts since for some jobs, chaining isn't an option. When your job hits the time limit, the batch system kills them and the command to submit a subsequent job is not processed.
PBS allows users to move the logic for chaining from the script and into the scheduler. This is done with a command line option:
$ qsub -W depend=afterok:<jobid> <job_script>
This tells the job scheduler that the script being submitted should not start until jobid completes successfully. The following conditions are supported:
- afterok:<jobid>
- Job is scheduled if the job <jobid> exits without errors or is successfully completed.
- afternotok:<jobid>
- Job is scheduled if job <jobid> exited with errors.
- afterany:<jobid>
- Job is scheduled if the job <jobid> exits with or without errors.
One method to simplify this process is to write multiple batch scripts, job1.pbs, job2.pbs, job3.pbs etc and submit them using the following script:
#!/bin/bash FIRST=$(qsub job1.pbs) echo $FIRST SECOND=$(qsub -W depend=afterany:$FIRST job2.pbs) echo $SECOND THIRD=$(qsub -W depend=afterany:$SECOND job3.pbs) echo $THIRD
Modify the script according to number of job chained jobs required. The Job <$FIRST> will be placed in queue while the jobs <$SECOND> and <$THIRD> will be placed in queue with the "Not Queued" (NQ) flag in Batch Hold. When <$FIRST> is completed, the NQ flag will be replaced with the "Queued" (Q) flag and will be moved to the active queue.
A few words of caution: If you list the dependency as "afterok"/"afternotok" and your job exits with/without errors then your subsequent jobs will be killed due to "dependency not met".
Resources
- The AutoDock home page has a variety of resources that may be of interest.
Last modified: September 10 2020 11:58:50.