Nextflow Registry | nf-core/apbs@0.0.0-0c7146d

nf-core/apbs @ 0.0.0-0c7146d

Compute biomolecular electrostatics by solving the Poisson-Boltzmann equation using APBS (Adaptive Poisson-Boltzmann Solver). Produces electrostatic potential maps and solvation energy values for large biomolecular assemblages.

electrostatics poisson-boltzmann solvation structural-biology biophysics computational-chemistry

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { APBS } from 'nf-core/apbs'

License

MIT License

Process

`Name`	`APBS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`apbs_input` file	APBS input configuration file specifying the electrostatics calculation, including paths to molecular structure files (PQR/PDB) and calculation parameters. The file extension is typically `.in` but `.inp` is also accepted for legacy purposes. `*.{in,inp}`
`pqr` file	One or more PQR molecular structure files referenced by the input configuration file. PQR files contain atomic coordinates, charges, and radii used by APBS for electrostatics calculations. `*.pqr`

Output 4 channels

#1 dx tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.dx` file	OpenDX format volumetric electrostatic potential map file output by APBS. Optional: this output is only produced when the input configuration file contains a `write pot dx <dx_filename>` directive. `*.dx`

#2 mc tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`io.mc` file	APBS multigrid calculation output file containing energy and force information from the finite difference solver. `io.mc`

#3 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.log` file	APBS standard output log file containing calculation results, including electrostatic solvation energies and run diagnostics. `*.log`

#4 versions_apbs tuple

`${task.process}` string	The name of the process
`apbs` string	The name of the tool
`apbs --version 2>&1 \| sed '6!d;s\|^.Version APBS \|\|; s\| .\$\|\|'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
apbs	APBS (Adaptive Poisson-Boltzmann Solver) is a software package for modelling biomolecular solvation through solution of the Poisson-Boltzmann equation. It computes electrostatic solvation energies and potentials for large biomolecular assemblages and is widely used in structural biology and computational biophysics.	https://www.poissonboltzmann.org/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:43:01 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fapbs/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/apbs/blobs/sha256:b0f6f5f82a6d5d69b11dcfade5ea3bbca7d9e3702379ca3c8efaa86fa7f3bb14
Size	3.1 KB
Checksum	sha256:b0f6f5f82a6d5d69b11dcfade5ea3bbca7d9e3702379ca3c8efaa86fa7f3bb14
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:02:35 (UTC)		3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 18:43:01 (UTC)		3	3.1 KB