.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH PDB2PQR30 "1" "June 2023" "pdb2pqr30 3.6.1+dfsg" "User Commands"
.SH NAME
pdb2pqr30 \- manual page for pdb2pqr30 3.6.1+dfsg
.SH DESCRIPTION
usage: pdb2pqr [\-h] [\-\-ff {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}]
.IP
[\-\-userff USERFF] [\-\-clean] [\-\-nodebump] [\-\-noopt]
[\-\-keep\-chain] [\-\-assign\-only]
[\-\-ffout {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}]
[\-\-usernames USERNAMES] [\-\-apbs\-input APBS_INPUT]
[\-\-pdb\-output PDB_OUTPUT] [\-\-ligand LIGAND] [\-\-whitespace]
[\-\-neutraln] [\-\-neutralc] [\-\-drop\-water] [\-\-include\-header]
[\-\-titration\-state\-method {propka}] [\-\-with\-ph PH]
[\-f FILENAMES] [\-r REFERENCE] [\-c CHAINS] [\-i TITRATE_ONLY]
[\-t THERMOPHILES] [\-a ALIGNMENT] [\-m MUTATIONS] [\-p PARAMETERS]
[\-\-log\-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [\-o PH]
[\-w WINDOW WINDOW WINDOW] [\-g GRID GRID GRID]
[\-\-mutator MUTATOR] [\-\-mutator\-option MUTATOR_OPTIONS] [\-d]
[\-l] [\-k] [\-q] [\-\-protonate\-all] [\-\-version]
input_path output_pqr
.PP
PDB2PQR v3.6.1: biomolecular structure conversion software.
.SS "positional arguments:"
.TP
input_path
Input PDB path or ID (to be retrieved from RCSB
database
.TP
output_pqr
Output PQR path
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.SS "Mandatory options:"
.IP
One of the following options must be used
.TP
\fB\-\-ff\fR {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}
The forcefield to use. (default: PARSE)
.TP
\fB\-\-userff\fR USERFF
The user\-created forcefield file to use. Requires
\fB\-\-usernames\fR and overrides \fB\-\-ff\fR (default: None)
.TP
\fB\-\-clean\fR
Do no optimization, atom addition, or parameter
assignment, just return the original PDB file in
aligned format. Overrides \fB\-\-ff\fR and \fB\-\-userff\fR (default:
False)
.SS "General options:"
.TP
\fB\-\-nodebump\fR
Do not perform the debumping operation (default: True)
.TP
\fB\-\-noopt\fR
Do not perform hydrogen optimization (default: True)
.TP
\fB\-\-keep\-chain\fR
Keep the chain ID in the output PQR file (default:
False)
.TP
\fB\-\-assign\-only\fR
Only assign charges and radii \- do not add atoms,
debump, or optimize. (default: False)
.TP
\fB\-\-ffout\fR {AMBER,CHARMM,PARSE,TYL06,PEOEPB,SWANSON}
Instead of using the standard canonical naming scheme
for residue and atom names, use the names from the
given forcefield (default: None)
.TP
\fB\-\-usernames\fR USERNAMES
The user\-created names file to use. Required if using
\fB\-\-userff\fR (default: None)
.TP
\fB\-\-apbs\-input\fR APBS_INPUT
Create a template APBS input file based on the
generated PQR file at the specified location.
(default: None)
.TP
\fB\-\-pdb\-output\fR PDB_OUTPUT
Create a PDB file based on input. This will be missing
charges and radii (default: None)
.TP
\fB\-\-ligand\fR LIGAND
Calculate the parameters for a single MOL2\-format
ligand at the path specified by this option. The MOL2
ligand name should match only one ligand in the PDB
file. (default: None)
.TP
\fB\-\-whitespace\fR
Insert whitespaces between atom name and residue name,
between x and y, and between y and z. (default: False)
.TP
\fB\-\-neutraln\fR
Make the N\-terminus of a protein neutral (default is
charged). Requires PARSE force field. (default: False)
.TP
\fB\-\-neutralc\fR
Make the C\-terminus of a protein neutral (default is
charged). Requires PARSE force field. (default: False)
.TP
\fB\-\-drop\-water\fR
Drop waters before processing biomolecule. (default:
False)
.TP
\fB\-\-include\-header\fR
Include pdb header in pqr file. WARNING: The resulting
PQR file will not work with APBS versions prior to 1.5
(default: False)
.SS "pKa options:"
.IP
Options for titration calculations
.TP
\fB\-\-titration\-state\-method\fR {propka}
Method used to calculate titration states. If a
titration state method is selected, titratable residue
charge states will be set by the pH value supplied by
\fB\-\-with_ph\fR (default: None)
.TP
\fB\-\-with\-ph\fR PH
pH values to use when applying the results of the
selected pH calculation method. (default: 7.0)
.SS "PROPKA invocation options:"
.TP
\fB\-f\fR FILENAMES, \fB\-\-file\fR FILENAMES
read data from <filename>, i.e. <filename> is added to
arguments (default: [])
.TP
\fB\-r\fR REFERENCE, \fB\-\-reference\fR REFERENCE
setting which reference to use for stability
calculations [neutral/low\-pH] (default: neutral)
.TP
\fB\-c\fR CHAINS, \fB\-\-chain\fR CHAINS
creating the protein with only a specified chain.
Specify " " for chains without ID [all] (default:
None)
.TP
\fB\-i\fR TITRATE_ONLY, \fB\-\-titrate_only\fR TITRATE_ONLY
Treat only the specified residues as titratable. Value
should be a comma\-separated list of "chain:resnum"
values; for example: \fB\-i\fR "A:10,A:11" (default: None)
.TP
\fB\-t\fR THERMOPHILES, \fB\-\-thermophile\fR THERMOPHILES
defining a thermophile filename; usually used in
\&'alignment\-mutations' (default: None)
.TP
\fB\-a\fR ALIGNMENT, \fB\-\-alignment\fR ALIGNMENT
alignment file connecting <filename> and <thermophile>
[<thermophile>.pir] (default: None)
.TP
\fB\-m\fR MUTATIONS, \fB\-\-mutation\fR MUTATIONS
specifying mutation labels which is used to modify
<filename> according to, e.g. N25R/N181D (default:
None)
.TP
\fB\-p\fR PARAMETERS, \fB\-\-parameters\fR PARAMETERS
set the parameter file [{default:s}] (default:
\fI\,/usr/lib/python3/dist\-packages/propka/propka.cfg\/\fP)
.TP
\fB\-\-log\-level\fR {DEBUG,INFO,WARNING,ERROR,CRITICAL}
logging level verbosity (default: INFO)
.TP
\fB\-o\fR PH, \fB\-\-pH\fR PH
setting pH\-value used in e.g. stability calculations
[7.0] (default: 7.0)
.TP
\fB\-w\fR WINDOW WINDOW WINDOW, \fB\-\-window\fR WINDOW WINDOW WINDOW
setting the pH\-window to show e.g. stability profiles
[0.0, 14.0, 1.0] (default: (0.0, 14.0, 1.0))
.TP
\fB\-g\fR GRID GRID GRID, \fB\-\-grid\fR GRID GRID GRID
setting the pH\-grid to calculate e.g. stability
related properties [0.0, 14.0, 0.1] (default: (0.0,
14.0, 0.1))
.TP
\fB\-\-mutator\fR MUTATOR
setting approach for mutating <filename>
[alignment/scwrl/jackal] (default: None)
.TP
\fB\-\-mutator\-option\fR MUTATOR_OPTIONS
setting property for mutator [e.g. type="side\-chain"]
(default: None)
.TP
\fB\-d\fR, \fB\-\-display\-coupled\-residues\fR
Displays alternative pKa values due to coupling of
titratable groups (default: False)
.TP
\fB\-l\fR, \fB\-\-reuse\-ligand\-mol2\-files\fR
Reuses the ligand mol2 files allowing the user to
alter ligand bond orders (default: False)
.TP
\fB\-k\fR, \fB\-\-keep\-protons\fR
Keep protons in input file (default: False)
.TP
\fB\-q\fR, \fB\-\-quiet\fR
suppress non\-warning messages (default: None)
.TP
\fB\-\-protonate\-all\fR
Protonate all atoms (will not influence pKa
calculation) (default: False)