Difference between revisions of "Pdb2pqr"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:modeling]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|pdb2pqr}} | |{{#vardefine:app|pdb2pqr}} | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 17:51, 15 August 2022
Description
The PDB2PQR tool is an interface for running PDB2PQR, which prepares structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Environment Modules
Run module spider pdb2pqr to find out what environment modules are available for this application.
System Variables
- HPC_PDB2PQR_DIR - installation directory
Citation
If you publish research that uses pdb2pqr you have to cite it as follows:
- PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5.
- PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7.