'\" t
.\"     Title: propka
.\"    Author: Manuel Prinz <debian@pinguinkiste.de>
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 2008-06-15
.\"    Manual: PROPKA Manual
.\"    Source: propka
.\"  Language: English
.\"
.TH "PROPKA" "1" "2008\-06\-15" "propka" "PROPKA Manual"
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.SH "NAME"
propka \- Protonate PDB files based on pKa
.SH "SYNOPSIS"
.HP \w'\fBpropka\fR\ 'u
\fBpropka\fR \fBPROPKATMP1\fR
.SH "DESCRIPTION"
.PP
\fBpropka\fR
automates the protonation (positioning of hydrogen ions) to a structure in
PDB
format for any given pKa value\&. The file to use has to be named
PROPKATMP1
in the directory where propka is run\&.
.PP
\fBpropka\fR
will generate two output files named
PROPKATMP2
and
PROPKATMP3\&.
PROPKATMP2
contains the resulting structure in
PDB
format\&.
PROPKATMP3
contains a summary of the
\fBpropka\fR
run\&.
.SH "CITING PROPKA"
.PP
Please acknowledge your use of
\fBpropka\fR
by citing:
.PP
Hui Li, Andrew D\&. Robertson, and Jan H\&. Jensen: Very Fast Empirical Prediction and Interpretation of Protein pKa Values, Proteins, 2005, 61, 704\-721\&.
.SH "WEB SERVICE"
.PP
PropKa can be used via a web interface at
\m[blue]\fBhttp://propka\&.ki\&.ku\&.dk/\fR\m[]\&.
.SH "SEE ALSO"
.PP
\fBpdb2pqr\fR(1)
.SH "AUTHOR"
.PP
\fBManuel Prinz\fR <\&debian@pinguinkiste\&.de\&>
.RS 4
Wrote this manpage for the Debian System\&.
.RE
.SH "COPYRIGHT"
.br
Copyright \(co 2008 Manuel Prinz
.br