What is a PDB to PDBQT converter used for?

A PDB to PDBQT converter prepares PDB coordinate text into a PDBQT-style format used in AutoDock and related molecular docking workflows. PDBQT adds atom type and charge fields to PDB-like coordinates.

What is the difference between PDB and PDBQT?

PDB stores atomic coordinates and structure records. PDBQT is a docking-oriented format that extends PDB-style coordinates with partial charge and AutoDock atom type information.

What does PDBQT format contain?

PDBQT keeps PDB-like atom coordinates and adds partial charge and AutoDock atom type fields. Ligand PDBQT files may also include ROOT, BRANCH, ENDBRANCH, TORSDOF, and torsion tree records.

Can I use this PDBQT output directly in AutoDock Vina?

This browser converter creates a fast PDBQT draft. For production AutoDock Vina docking, review protonation, hydrogens, charges, atom types, receptor cleanup, ligand rotatable bonds, and torsion definitions in a docking preparation workflow.

Can I convert PDBQT back to PDB?

A PDBQT file can often be reduced to PDB-like coordinate records by removing docking-specific charge, atom type, and torsion metadata, but PDB cannot preserve AutoDock torsion tree information.

PDB to PDBQT Converter Online

Paste a PDB structure, upload a .pdb file, or import a structure by PDB ID from the Protein Data Bank, then convert it into PDBQT for docking pipelines. This browser tool adds element and charge/type columns in PDBQT layout for fast preparation.

Quick answer: PDB stores structure coordinates, while PDBQT is a docking format that includes PDB-style coordinates plus partial charge and AutoDock atom type fields. Use this tool for a quick PDBQT draft from pasted text, a local PDB file, or an RCSB PDB ID before deeper ligand or receptor preparation.

PDB Input

Upload .pdb file

Paste PDB text, upload a local PDB file, or enter a 4-character PDB ID.

PDBQT Output

Ready.

Notes for Docking Workflows

This tool creates a practical PDBQT text layout directly in-browser for rapid prototyping.
For production docking runs, you can further refine protonation state and torsion definitions in your docking suite.
Use this page as a quick conversion utility when you need a fast PDBQT draft structure.

How to convert PDB to PDBQT online

Paste PDB text, upload a local .pdb file, or type a 4-character PDB ID such as 1CRN.
Click Convert to PDBQT. The converter keeps ATOM/HETATM coordinates and writes PDBQT-style charge and AutoDock atom type fields.
Copy or download the generated .pdbqt file for docking preparation, quick checks, or teaching examples.
Before a real docking run, review hydrogens, protonation, charges, atom types, flexible bonds, and receptor cleanup in your docking workflow.

PDB vs PDBQT

PDB is a general structural biology coordinate format. PDBQT is commonly used by AutoDock-style docking tools because it carries atom typing and partial charge information needed during docking calculations.

Format	What it stores	Common use
PDB	Atom names, residue names, chains, coordinates, occupancy, B-factor, and element symbols.	Protein structures, ligands, crystallography files, visualization, and structural biology exchange.
PDBQ	PDB-like coordinates plus partial charge information.	Older docking preparation workflows where charge is needed but AutoDock atom type is not stored as in PDBQT.
PDBQT	PDB-like coordinates plus partial charge and AutoDock atom type fields. Ligands may include torsion tree records.	AutoDock, AutoDock Vina, docking pipelines, ligand/receptor preparation, and docking tutorials.

Related docking and structure tools

PDBQT Format Explained

A PDBQT file looks similar to a PDB file, but docking tools read extra fields near the end of each atom line. The Q part represents partial charge, and the T part represents the AutoDock atom type.

ATOM      1  N   ALA A   1      11.104  13.207   9.142  1.00 20.00    -0.346  N
ATOM      2  CA  ALA A   1      12.560  13.320   9.420  1.00 20.00     0.186  C
HETATM    3  O   LIG L   1      10.440  11.980   8.500  1.00 20.00    -0.508 OA

Atom types

AutoDock atom types such as C, N, OA, SA, HD, Cl, and Zn tell docking software how each atom should be interpreted during scoring.

Charges

PDBQT stores partial charges. This quick browser converter writes a neutral draft charge field, so production docking should still assign appropriate charges with a dedicated preparation tool.

Torsions

Flexible ligand PDBQT files can include ROOT, BRANCH, ENDBRANCH, and TORSDOF records to describe rotatable bonds and torsion degrees of freedom.

Receptors vs ligands

Receptor PDBQT preparation usually focuses on cleanup, hydrogens, charges, and atom types. Ligand PDBQT preparation also needs rotatable bond and torsion tree handling.

Important: MolDraw's browser output is a fast PDBQT draft. For AutoDock Vina production work, validate the protonation state, missing atoms, alternate locations, waters, metals, cofactors, charge model, atom typing, and ligand flexibility.

AutoDock Vina PDBQT Checklist

Use this checklist when preparing PDBQT files for AutoDock, AutoDock Vina, or related docking workflows.

Clean the PDB: remove irrelevant waters, duplicated chains, alternate conformations, and non-target ligands unless they are needed.
Add hydrogens: docking scores are sensitive to hydrogen placement, especially polar hydrogens and hydrogen-bond donors.
Check protonation: choose the protonation state expected at your assay pH or biological condition.
Assign charges: use a docking preparation workflow for realistic partial charges before final docking.
Review atom types: metals, halogens, sulfur, phosphorus, and charged atoms may need careful atom typing.
Handle torsions: ligand PDBQT files should define rotatable bonds correctly; receptor files are usually rigid unless flexible side chains are prepared separately.
Validate the output: open the PDBQT in your docking or visualization tool before launching a long batch job.

PDBQT to PDB: what happens in reverse?

Searches such as PDBQT to PDB converter usually mean the user wants a simple coordinate file for viewing. A PDBQT file can often be reduced back to PDB-like ATOM/HETATM records by removing charge, atom type, and torsion tree metadata. However, PDB cannot preserve AutoDock-specific records such as ROOT, BRANCH, ENDBRANCH, and TORSDOF.

Common Questions

Is PDBQT the same as PDB?

No. PDB is a general coordinate format. PDBQT is a docking format that adds partial charge and AutoDock atom type fields, and may include torsion tree information for flexible ligands.

Why do AutoDock and Vina need PDBQT?

Docking programs need atom typing and charge information for scoring and interaction evaluation. PDB alone usually does not contain enough docking-specific information.

Does this tool calculate real Gasteiger charges?

No. This page creates a quick browser-side PDBQT draft with a neutral charge field. Use a full docking preparation workflow for final charge assignment.

Can I import directly from the Protein Data Bank?

Yes. Enter a 4-character PDB ID, such as 1CRN, and the tool imports the PDB file from RCSB before generating the PDBQT draft.