pdb2pqr - Online in the Cloud

PROGRAM:

NAME

pdb2pqr - Generate PQR files for use in electrostatics calculations

SYNOPSIS

pdb2pqr [--nodebump] [--noopt] [--chain] [--assign-only] [--clean] [--ffout=name]
[--with-ph=ph] [--apbs-input] [--ligand=path] [[--verbose] | [-v]] --ff=forcefield
path output-path

pdb2pqr {--help | -h}

DESCRIPTION

pdb2pqr automates many of the common tasks of preparing structures for continuum
electrostatics calculations, providing a utility for converting protein files in PDB
format (path) to PQR format (output-path). These tasks include:

· Adding a limited number of missing heavy atoms to biomolecular structures

· Determining side-chain pKas

· Placing missing hydrogens

· Optimizing the protein for favorable hydrogen bonding

· Assigning charge and radius parameters from a variety of force fields

OPTIONS

pdb2pqr accepts the following options:

--ff=forcefield
The forcefield to use. Current values are amber, charm, parse and tyl06.

--help, -h
Print a help message and exit.

--nodebump
Do not perform debumping operation.

--noopt
Do not perform hydrogen optimization.

--chain
Keep the chain ID in the output PQR file.

--assign-only
Only assigns charges to add atoms, debump, or optimize.

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

--ffout=name
Instead of using the standard caninical 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.

--apbs-input
Create an APBS input file based on the generated PQR file. Also create a Python pickle
for using these parameters in other programs.

--ligand=path
Calculate the parameters for the ligand in MOL2 format at the given path. Pdb2pka must
be compiled.

--verbose, -v
Print additional information to screen.

EXTENSIONS

Extensions add functionality to PDB2PQR and are called by passing a parameter to pdb2pqr.
They put their results into files located in output-path.

The following extensions can be used by pdb2pqr:

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

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

--hbond
Print a list of hygrogen bonds to output-path.hbond.

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

--contact
Print a list of contacts to output-path.con.

--hbondwhatif
Print a list of hydrogen bonds to output-path.hbo.

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

--rama
Print the per-residue phi and psi angles to outpath-path.rama.

CITING PDB2PQR

Please acknowledge your use of pdb2pqr by citing:

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the
setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic
Acids Research, 32, W665-W667 (2004).

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