PDB2PQR¶
PDB2PQR automates many tasks to prepare structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. The bundle packages version 3.6.1.
Usage example¶
The following command can be executed in the terminal to load the bundle:
The module makes the following commands available:
The pdb2pqr_shell command can be used to access a shell in the bundle.
Run pet list -t pdb2pqr for a list of examples.
Performance notes¶
No performance notes available
Recommended resources¶
PDB2PQR should be run on a system with at least 8 GB of RAM and 2 threads.
Benchmarks¶
No benchmarks available.
Community guides and tutorials¶
- No community guides available.
Official site and documentation¶
Licensing information¶
PDB2PQR uses a custom license.
Primary citation¶
Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci, 27 (1), 112-128, 2018. doi
External guides and resources¶
- If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za