Command line usage

The command line version of PDB2PQR must be installed from source using the instructions in the PDB2PQR installation and availability section. This version of the software offers an expanded range of options and can also be customized with user extensions.

The command line PDB2PQR is invoked as

   $ python pdb2pqr.py [options] --ff={forcefield} {path} {output-path}

The required arguments are as follows:

forcefield

The forcefield to use -- currently AMBER (AMBER99, Wang J, et al, 2000), CHARMM (CHARMM27, MacKerell AD Jr, et al, 1998), PARSE (PARSE, Sitkoff D, et al, 1994), and TYL06 (Tan C, et al, 2006) are supported.

path

The path to the PDB file or an ID to obtain from the PDB archive

output-path

The desired output name of the PQR file to be generated

Optional command-line arguments are:

--nodebump

Do not perform the debumping operation

--noopt

Do not perform hydrogen bonding network optimization

--chain

Keep the chain ID in the output PQR file

--assign-only

Only assign charges and radii - do not add atoms, debump, or optimize.

--clean

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

--ffout=<name>

Instead of using the standard canonical naming scheme for residue and atom names, use the names from the given forcefield.

--with-ph=<ph>

Use PROPKA to calculate pKas and apply them to the molecule given the pH value. Actual PROPKA results will be output to <output-path>.propka.

--ligand=<mol2 file>

Use the PDB2PKA package to generate parameters for the specific ligand in MOL2 format. MOL2-format ligands can be generated using PROPDRG server or from within some molecular modeling packages

--apbs-input

Create a template APBS input file based on the generated PQR file.

--whitespace

Put an extra whitespace between atom name and residue name to <output-path>-whitespace.pqr, this may (or may not) break strict PDB formatting and cause problems for some visualization programs.

--verbose (-v)

Print information to stdout

--help (-h)

Display the usage information

Additional optional command-line arguments from the extensions directory are:

--chi

Print the per-residue backbone chi angle to <output-path>.chi

--phi

Print the per-residue backbone phi angle to <output-path>.phi

--psi

Print the per-residue backbone psi angle to <output-path>.psi

--rama

Print the per-residue phi and psi angles to <output-path>.rama for Ramachandran plots

--hbond

Print a list of hydrogen bonds to <output-path>.hbond

--salt

Print a list of salt bridges to <output-path>.salt