Molecular File Converter
Convert between chemical file formats with our web-based tool
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Our PDB to PDBQT Converter is a web-based tool that prepares your protein or ligand files for molecular docking simulations. It converts PDB files to the PDBQT format, which includes essential information such as atomic charges and atom types required by popular docking software, such as AutoDock Vina.
How to use
- Upload Your File: Click “Upload File” or drag and drop your file directly into the designated area. You can also paste the file’s content using the “Paste Data” option.
- Choose Your Formats: Use the “Input Format” and “Output Format” dropdown menus to select the conversion you need. Make sure PDB (Protein Data Bank format) is selected as the input and PDBQT (AutoDock PDBQT format) as the output.
- Start the Conversion: Press the “Convert File” button to begin the process. The tool will process your file instantly.
- Download Your File: Once the conversion is complete, a download link for your new file will appear. Click it to save the file to your device.
Input, Output, and Key Changes
Understanding the transformation from PDB to PDBQT is key to effective molecular docking. Here’s a breakdown of the formats and the changes that occur in each.
Sample input (PDB Format)
The PDB format is a standard for 3D structural data of large biological molecules, such as proteins and nucleic acids. It contains atomic coordinates but lacks information on partial charges or atom types needed for docking. Example of a PDB file:
ATOM 1 N ALA A 1 27.222 18.238 35.532 1.00 28.80 N”
Sample Output (PDBQT Format)
The PDBQT format is an extension of PDB used by AutoDock and AutoDock Vina. In addition to atomic coordinates, it includes partial charges (Q) and AutoDock atom types (T), making the structure suitable for docking simulations.
After conversion, the same atom is annotated with charge and atom type information. Example PDBQT line:
ATOM 1 N ALA A 1 27.222 18.238 35.532 -0.347 NA
Changes in the Conversion Process
The conversion from PDB to PDBQT involves several critical modifications to prepare the molecule for docking:
- Addition of Partial Charges: The most significant change is the addition of a partial charge for each atom. In the example above, +0.193 was added. This is essential for calculating electrostatic interactions between the ligand and the protein.
- Assignment of Atom Types: The last column now includes an AutoDock-specific atom type (e.g., N for Nitrogen). This helps the docking software identify atoms and apply the correct energy parameters.
- Addition of Hydrogens: The tool typically adds polar hydrogens to the structure if they are missing, as these are critical for forming hydrogen bonds.
- Metadata for Torsion: For ligands, the PDBQT file includes metadata (ROOT, BRANCH, ENDBRANCH) that define rotatable bonds, enabling flexible docking.
FAQ
Reference
O’Boyle, N.M., Banck, M., James, C.A. et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011). https://doi.org/10.1186/1758-2946-3-33
Meet the Authors
Mahdi Morshedi Yekta
Founder & Bioinformatics Developer
Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.
Fatemeh Faryadras
Medical Biotechnologist & Researcher
Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.
Dr. Mosayeb Rostamian
Assistant Professor, Infectious Diseases Research Center
Certified Scientific Reviewer
Google ScholarExpert Review Process
To ensure the highest quality and scientific accuracy, this tool's underlying algorithms, formulas, and edge-case handling have been thoroughly reviewed and validated by Dr. Mosayeb Rostamian.
The "Reviewed By" badge signifies that an independent expert has evaluated the tool's logic to guarantee accuracy and alignment with the current consensus in the scientific community.