PDB2PQR
PDB2PQR converts PDB files to PQR format, adding missing atoms and assigning charges for electrostatics calculations.
PDB2PQR is an online tool designed to prepare structures from the Protein Data Bank (PDB) for electrostatics calculations. It provides a streamlined process to convert PDB files into PQR files, which are used as input for various computational biology and chemistry applications. Can also be used to fix common issue with PDB files.
Estimated resource cost: 0.000124
Categories: Utilities & Conversions
Tags: File Conversion Proteins Structure Fixing
Key Capabilities
- Converts PDB files to PQR format.
- Automatically adds missing heavy atoms and hydrogens.
- Optimizes the hydrogen bonding network.
- Assigns atomic charges and radii using multiple force fields (e.g., AMBER, CHARMM, PARSE, PEOEPB).
- Allows specification of force field.
- Predicts protonation states of titratable groups based on pKa calculations.
- Enables setting of pH for protonation state predictions.
- Provides options for optimizing hydrogen bonds.
- Produces PQR files with atomic coordinates, partial charges, and radii.
- Compatible with other computational tools for electrostatics calculations and molecular simulations.
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 18 |
| runtime_median | 6 |
| runtime_std | 212 |
| runtime_90th_percentile | 12 |
| runtime_max | 4456 |
Similar Tools
- PDB-SDF Converter
- PDB-mmCIF Converter
- PDBFixer
- ClusterProt
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.000124
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.