.TH AUTODOCK "1" "November 2010" "AutoDock Vina 1.1.1 (Apr 20, 2010)"
.SH NAME
vina \- docking small molecules against proteins
.SH DESCRIPTION
.SS "Input:"
.TP
\fB\-\-receptor\fR arg
rigid part of the receptor (PDBQT)
.TP
\fB\-\-flex\fR arg
flexible side chains, if any (PDBQT)
.TP
\fB\-\-ligand\fR arg
ligand (PDBQT)
.SS "Search space (required):"
.TP
\fB\-\-center_x\fR arg
X coordinate of the center
.TP
\fB\-\-center_y\fR arg
Y coordinate of the center
.TP
\fB\-\-center_z\fR arg
Z coordinate of the center
.TP
\fB\-\-size_x\fR arg
size in the X dimension (Angstroms)
.TP
\fB\-\-size_y\fR arg
size in the Y dimension (Angstroms)
.TP
\fB\-\-size_z\fR arg
size in the Z dimension (Angstroms)
.SS "Output (optional):"
.TP
\fB\-\-out\fR arg
output models (PDBQT), the default is chosen based on
the ligand file name
.TP
\fB\-\-log\fR arg
optionally, write log file
.SS "Misc (optional):"
.TP
\fB\-\-cpu\fR arg
the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
.TP
\fB\-\-seed\fR arg
explicit random seed
.TP
\fB\-\-exhaustiveness\fR arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
.TP
\fB\-\-num_modes\fR arg (=9)
maximum number of binding modes to generate
.TP
\fB\-\-energy_range\fR arg (=3)
maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)
.SS "Configuration file (optional):"
.TP
\fB\-\-config\fR arg
the above options can be put here
.SS "Information (optional):"
.TP
\fB\-\-help\fR
display usage summary
.TP
\fB\-\-help_advanced\fR
display usage summary with advanced options
.TP
\fB\-\-version\fR
display program version
.SH "SEE ALSO"
AutoDock Vina home page on http://vina.scripps.edu.