Use PDB2PQR

Official Neurosnap webserver for accessing PDB2PQR online.

Protein Design Molecular Dynamics

Overview

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.

Neurosnap Overview

The PDB2PQR online webserver allows anybody with a Neurosnap account to run and access PDB2PQR, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • 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.
  • Can be integrated into custom pipelines and automation scripts.
  • Handles a wide range of PDB structures, including those with non-standard residues and ligands.

Statistics

Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.

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API Request

Access PDB2PQR using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.

Job Note

Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.

Configuration & Options

The input protein structure to convert or clean using PDB2PQR.

Core Settings

For most applications, the choice is easy: PARSE. This forcefield has been optimized for implicit solvent calculation and is probably the best choice for visualization of biomolecular electrostatics and many common types of energetic calculations for biomolecules. However, AMBER and CHARMM may be more appropriate if you are attempting to compare directly to simulations performed with those force fields, require nucleic acid support, are simulating ligands parameterized with those force fields, etc...

Do no optimization, atom addition, or parameter assignment, just return the original PDB file in aligned format.

Drop waters before processing biomolecule.

Make the N-terminus of a protein neutral (default is charged). Requires PARSE force field.

Make the C-terminus of a protein neutral (default is charged). Requires PARSE force field.

When checked, ensures that new atoms are not rebuilt too close to existing atoms.

When checked, optimize the hydrogen bonding network.

pKa Options

Method used to calculate titration states. If a titration state method is selected, titratable residue charge states will be set by the pH value below.

The specified pH value to use when applying the results of the selected pH calculation method and for which to select protonation states.

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