From the documentation

The use of continuum solvation methods such as APBS requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to these structures. To address this problem, we have developed PDB2PQR. This software automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.

References:

• E. Jurrus, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 PubMed  |  PMC  |  Journal
• T. J. Dolinsky, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 2007 PubMed  |  PMC  |  Journal

• pdb2pqr on GitHub
• Home page
• Manual

• Module Name: pdb2pqr (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=2g
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]$ pdb2pqr --include-header --ff PARSE --with-ph=7.4 --drop-water 1FAS 1FAS.pqr
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. pdb2pqr.sh), which uses the input file 'pdb2pqr.in'. For example:

#!/bin/bash
module load pdb2pqr/3.6.1
pdb2pqr --include-header --ff PARSE --with-ph=7.4 --drop-water 1FAS 1FAS.pqr

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=2g --time 2 --partition=quick pdb2pqr.sh

Create a swarmfile (e.g. pdb2pqr.swarm). For example:

pdb2pqr --include-header --ff PARSE --with-ph=7.4 --drop-water 1FAS 1FAS.pqr
pdb2pqr --include-header --ff PARSE --with-ph=7.4 --drop-water 5EDU 5EDU.pqr
pdb2pqr --include-header --ff PARSE --with-ph=7.4 --drop-water 3C10 3C10.pqr

Submit this job using the swarm command.

swarm -f pdb2pqr.swarm -g 2 -t 1 -b3 --time 2 --partition=quick --module pdb2pqr/3.6.1