You provide a protein structure — as a PDB ID, raw PDB data, or an S3 URI — plus a target pH. The pH is the parameter that most affects your result: it drives which titratable residues get protonated, so set it to the environment you care about (7.4 for physiological, lower for endosomal or gastric contexts).

PDB2PQR inputs and parameters

Structure input

Parameter	Type	Required	Description
`pdb_id`	string	One of three (chat only)	Four-character PDB accession code (e.g., `"1M17"`). The platform resolves this to the structure before dispatch — it is not a field the backend API accepts directly.
`pdb_content`	string	One of three	PDB file contents as a string
`pdb_s3_uri`	string	One of three	S3 URI to an already-uploaded or previously-downloaded PDB file

Exactly one of pdb_content or pdb_s3_uri must reach the backend job (the chat tool also accepts pdb_id, which the platform resolves to one of the other two first).

Core parameters

Parameter	Type	Default	Description
`ph`	number	`7.4`	Target pH for protonation state assignment (0.0-14.0)
`forcefield`	string	`"amber"`	Force field for charge/radius assignment

pKa prediction always uses PROPKA — there is no user-selectable titration-state method.

Force field options

Value	Description
`"amber"` (default)	AMBER ff14SB, general purpose / MD preparation
`"charmm"`	CHARMM36 parameters
`"parse"`	Optimized for Poisson-Boltzmann electrostatics
`"swanson"`	Extended AMBER for nucleic acid-protein complexes
`"peoepb"`	PB-optimized partial charges for APBS
`"tyl06"`	Tyrosine-focused parameters

Processing options

Parameter	Type	Default	Description
`include_hydrogens`	boolean	`true`	Add missing hydrogens to the structure
`optimize_hydrogen_bonds`	boolean	`true`	Optimize the hydrogen-bonding network
`assign_charges`	boolean	`true`	Assign partial charges from the chosen force field
`debump`	boolean	`true`	Resolve steric clashes introduced by added hydrogens
`remove_water`	boolean	`true`	Remove crystallographic water molecules
`chain_ids`	string[]	`null` (all chains)	Process only the listed chain IDs (e.g., `["A"]`)

Output options

Parameter	Type	Default	Description
`output_format`	string	`"pqr"`	`"pqr"` (charges and radii) or `"pdb"` (also writes a companion PDB file)
`include_propka_output`	boolean	`true`	Include the full PROPKA pKa-prediction output
`pdb_filename`	string	`"input.pdb"`	Filename recorded for tracking; has no effect on processing

Common pH values

pH	Context
7.4	Physiological (blood, most in vitro assays)
7.0	Standard neutral
5.0	Endosomal/lysosomal pH
6.5	Tumor microenvironment
4.5	Gastric pH

Input validation rules

PDB ID must be a valid four-character alphanumeric code
pH must be between 0.0 and 14.0
PDB content must contain valid ATOM/HETATM records
Force field name must be lowercase ("amber", not "AMBER")

Input from previous jobs

Source Tool	Extracted Field
PDB Search	PDB ID or structure file
ESMFold	Predicted PDB structure
Biotite	Processed structure file

PDB2PQR inputs and parameters