'\" t
.\"     Title: pdb2pqr
.\"    Author: Manuel Prinz <debian@pinguinkiste.de>
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 2008-06-04
.\"    Manual: PDB2PQR Manual
.\"    Source: pdb2pqr
.\"  Language: English
.\"
.TH "PDB2PQR" "1" "2008\-06\-04" "pdb2pqr" "PDB2PQR Manual"
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.SH "NAME"
pdb2pqr \- Generate PQR files for use in electrostatics calculations
.SH "SYNOPSIS"
.HP \w'\fBpdb2pqr\fR\ 'u
\fBpdb2pqr\fR [\fB\-\-nodebump\fR] [\fB\-\-noopt\fR] [\fB\-\-chain\fR] [\fB\-\-assign\-only\fR] [\fB\-\-clean\fR] [\fB\-\-ffout=\fR\fB\fIname\fR\fR] [\fB\-\-with\-ph=\fR\fB\fIph\fR\fR] [\fB\-\-apbs\-input\fR] [\fB\-\-ligand=\fR\fB\fIpath\fR\fR] [[\fB\-\-verbose\fR] | [\fB\-v\fR]] \fB\-\-ff=\fR\fB\fIforcefield\fR\fR \fB\fIpath\fR\fR \fB\fIoutput\-path\fR\fR
.HP \w'\fBpdb2pqr\fR\ 'u
\fBpdb2pqr\fR {\fB\-\-help\fR | \fB\-h\fR}
.SH "DESCRIPTION"
.PP
\fBpdb2pqr\fR
automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a utility for converting protein files in
PDB
format (\fIpath\fR) to
PQR
format (\fIoutput\-path\fR)\&. These tasks include:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Adding a limited number of missing heavy atoms to biomolecular structures
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Determining side\-chain pKas
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Placing missing hydrogens
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Optimizing the protein for favorable hydrogen bonding
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Assigning charge and radius parameters from a variety of force fields
.RE
.SH "OPTIONS"
.PP
\fBpdb2pqr\fR
accepts the following options:
.PP
\fB\-\-ff=\fR\fB\fIforcefield\fR\fR
.RS 4
The
\fIforcefield\fR
to use\&. Current values are
\fBamber\fR,
\fBcharm\fR,
\fBparse\fR
and
\fBtyl06\fR\&.
.RE
.PP
\fB\-\-help\fR, \fB\-h\fR
.RS 4
Print a help message and exit\&.
.RE
.PP
\fB\-\-nodebump\fR
.RS 4
Do not perform debumping operation\&.
.RE
.PP
\fB\-\-noopt\fR
.RS 4
Do not perform hydrogen optimization\&.
.RE
.PP
\fB\-\-chain\fR
.RS 4
Keep the chain ID in the output PQR file\&.
.RE
.PP
\fB\-\-assign\-only\fR
.RS 4
Only assigns charges to add atoms, debump, or optimize\&.
.RE
.PP
\fB\-\-clean\fR
.RS 4
Do no optimization, atom addition, or parameter assignment, just return the original
PDB
file in aligned format\&.
.RE
.PP
\fB\-\-ffout=\fR\fB\fIname\fR\fR
.RS 4
Instead of using the standard caninical naming scheme for residue and atom names, use the names from the given forcefield\&.
.RE
.PP
\fB\-\-with\-ph=\fR\fB\fIph\fR\fR
.RS 4
Use
\fBpropka\fR
to calculate pKas and apply them to the molecule given the pH value\&. Actual PropKa results will be output to
\fIoutput\-path\fR\&.propka\&.
.RE
.PP
\fB\-\-apbs\-input\fR
.RS 4
Create an APBS input file based on the generated PQR file\&. Also create a Python pickle for using these parameters in other programs\&.
.RE
.PP
\fB\-\-ligand=\fR\fB\fIpath\fR\fR
.RS 4
Calculate the parameters for the ligand in MOL2 format at the given
\fIpath\fR\&. Pdb2pka must be compiled\&.
.RE
.PP
\fB\-\-verbose\fR, \fB\-v\fR
.RS 4
Print additional information to screen\&.
.RE
.SH "EXTENSIONS"
.PP
Extensions add functionality to PDB2PQR and are called by passing a parameter to
\fBpdb2pqr\fR\&. They put their results into files located in
\fIoutput\-path\fR\&.
.PP
The following extensions can be used by
\fBpdb2pqr\fR:
.PP
\fB\-\-phi\fR
.RS 4
Print the per\-residue backbone phi angle to
\fIoutput\-path\fR\&.phi\&.
.RE
.PP
\fB\-\-psi\fR
.RS 4
Print the per\-residue backbone psi angle to
\fIoutput\-path\fR\&.phi\&.
.RE
.PP
\fB\-\-hbond\fR
.RS 4
Print a list of hygrogen bonds to
\fIoutput\-path\fR\&.hbond\&.
.RE
.PP
\fB\-\-chi\fR
.RS 4
Print the per\-residue backbone chi angle to
\fIoutput\-path\fR\&.chi\&.
.RE
.PP
\fB\-\-contact\fR
.RS 4
Print a list of contacts to
\fIoutput\-path\fR\&.con\&.
.RE
.PP
\fB\-\-hbondwhatif\fR
.RS 4
Print a list of hydrogen bonds to
\fIoutput\-path\fR\&.hbo\&.
.RE
.PP
\fB\-\-salt\fR
.RS 4
Print a list of salt bridges to
\fIoutput\-path\fR\&.salt\&.
.RE
.PP
\fB\-\-rama\fR
.RS 4
Print the per\-residue phi and psi angles to
\fIoutpath\-path\fR\&.rama\&.
.RE
.SH "CITING PDB2PQR"
.PP
Please acknowledge your use of
\fBpdb2pqr\fR
by citing:
.PP
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)\&.
.SH "SEE ALSO"
.PP
\fBpsize\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