Receptor Prep (PDBFixer)¶

OpenMM's PDBFixer is a Python library for preparing molecular structures for simulations, particularly when working with files in the Protein Data Bank (PDB) format. It can address common issues such as missing heavy atoms, hydrogen atoms, or residues, and can add missing chains or fix terminal capping. It is often used in the preprocessing phase of molecular dynamics simulations.

File Inputs:¶

PDB File¶

A PDB file containing the structure of the molecule or system to be fixed.

Parameters¶

`addMissingResidues`¶

Type	Default
Bool	true

Whether to add missing residues based on the structure and sequence.

`addMissingAtoms`¶

Type	Default
Bool	true

`addMissingHydrogens`¶

Type	Default
Bool	true

Whether to add hydrogen atoms to the structure, with optional control over pH for titration states.

`pH`¶

Type	Default
Float	true

`removeHeterogens`¶

Type	Default
Bool	true

Whether to remove small molecules or ions from the structure, with options to retain water molecules.

`removeWater`¶

Type	Default
Bool	true

Running on Deep Origin¶

To run this tool on Deep Origin, follow these steps:

1. Create a database to store input and output files¶

Navigate to DataHub on Deep Origin, and create a database for this tool. Add columns for input and output files. Create a new row and upload your input files to the input column.

This image shows an example database:

2. Start a tool run on Deep Origin¶

For this tool run, we will use the following parameters:

To start a tool run, use:

from deeporigin.tools import run

job_id = run.receptor_prep(
    database_id="<your-db-name>",
    row_id="<row-name>",
    output_column_name="<output-column-name>",
    receptor_column_name="<receptor-column-name>",
    ligand_column_name="<ligand-column-name>",
    add_missing_residues=True,
    add_missing_atoms= True,
    add_missing_hydrogens= True,
    ph = 7.4,
    remove_heterogens= True,
    remove_water= True,
)

run.receptor_prep returns the ID of the tool run, that can be used to monitor the status of the run and terminate it if needed.

run.receptor_prep prints a message that looks like:

🧬 Job started with ID: 9f7a3741-e392-45fb-a349-804b7fca07d7

File Outputs:¶

Fixed PDB File¶

The corrected and prepared molecular structure, which can be saved as a PDB file.