.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH PROPKA3 "1" "January 2024" "propka3 3.5.1" "User Commands"
.SH NAME
propka3 \- predict pKa values of ionizable groups
.SH DESCRIPTION
usage: propka3 [\-h] [\-f FILENAMES] [\-r REFERENCE] [\-c CHAINS]
.IP
[\-i TITRATE_ONLY] [\-t THERMOPHILES] [\-a ALIGNMENT]
[\-m MUTATIONS] [\-\-version] [\-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]
input_pdb
.PP
PROPKA predicts the pKa values of ionizable groups in proteins and proteinligand complexes based in the 3D structure
.SS "positional arguments:"
.TP
input_pdb
read data from <filename>
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.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\-\-version\fR
show program's version number and exit
.TP
\fB\-p\fR PARAMETERS, \fB\-\-parameters\fR PARAMETERS
set the parameter file (default: \fI\,/build/reproduciblepath/propka\-3.5.1/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)