Adaptive Poisson-Boltzmann Solver (APBS)
Overview
Solves the equations of continuum electrostatics for large biomolecular assemblages.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | apbs/3.1.3 |
| BGSC | apbs/3.1.4 |
Note: You can simply use module load apbs to activate the most recently installed version of this software.
Arguments / Options
This is a list of arguments for the apbs command that we wanted to highlight. See Resources for more.
| Option | Description |
|---|---|
| --help | displays the help page |
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load apbs # Load APBS
apbs myfile.in
Real Example
Has your research group used APBS in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of APBS.
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001.