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

References:

• Chen R, Li L, Weng Z ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) Jul 1;52(1):80-7.

• ZDOCK Main Site

• Module Name: zdock (see the modules page for more information)
• zdock/3.0.2: single-threaded
• zdock/3.0.2_mpi: MPI
• Environment variables set
  • ZDOCK_HOME
  • OMPI_MCA_btl

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 ~]$ cp $ZDOCK_HOME/uniCHARMM . 
[user@cn3144 ~]$ 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 ~]$ cp $ZDOCK_HOME/create_lig . 
[user@cn3144 ~]$ create.pl zdock.out 

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

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

#!/bin/bash
set -e
module load zdock/3.0.2_mpi
cp $ZDOCK_HOME/uniCHARMM .
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
cp $ZDOCK_HOME/create_lig .
create.pl zdock.out

Submit this job using the Slurm sbatch command.

sbatch --ntasks=16 zdock.sh