Biowulf High Performance Computing at the NIH
ZDOCK on Biowulf

zDOCK performs a full rigid-body search of docking orientations between two proteins. This includes performance optimization and a novel pairwise statistical energy potential.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load zdock

[user@cn3144 ~]$ zgrep ^ATOM /pdb/pdb/cg/pdb1cgi.ent.gz | grep ' E ' > 1cgi_r.pdb 
[user@cn3144 ~]$ zgrep ^ATOM /pdb/pdb/cg/pdb1cgi.ent.gz | grep ' I ' > 1cgi_l.pdb 
[user@cn3144 ~]$ ln -s $ZDOCK_HOME/uniCHARMM . 
[user@cn3144 ~]$ mark_sur 1cgi_r.pdb 1cgi_r_m.pdb 
[user@cn3144 ~]$ mark_sur 1cgi_l.pdb 1cgi_l_m.pdb 
[user@cn3144 ~]$ zdock -R 1cgi_r_m.pdb -L 1cgi_l_m.pdb -o zdock.out 
[user@cn3144 ~]$ ln -s $ZDOCK_HOME/create_lig . 
[user@cn3144 ~]$ zdock.out 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load zdock/3.0.2_mpi
mark_sur receptor.pdb receptor_m.pdb
mark_sur ligand.pdb ligand_m.pdb
srun --mpi=pmix zdock -R receptor_m.pdb -L ligand_m.pdb -o zdock.out
ln -s $ZDOCK_HOME/create_lig . zdock.out

Submit this job using the Slurm sbatch command.

sbatch --ntasks=16