AutoDock can be run in "command mode", using the "
-c
" flag thus:
% autodock3 -p lig.macro.dpf -l lig.macro.clg -c
When AutoDock has read in the grid maps specified in "
lig.macro.dpf
", the program gives the message "COMMAND MODE" and waits for the user to issue a command from the
standard input
. These commands are described in more detail below.
An alternative way of using the command mode is to edit a file containing the commands you wish
AutoDock
to execute (say "
command.file
") and channel the output to a file (say "
command.output
"), thus:
% autodock3 -p lig.macro.dpf -l lig.macro.clg -c < command.file > command.output &
AutoDock can also be used in a UNIX pipe command. This is valuable when an alternative search procedure is desired. Here, the alternative search procedure
issues commands to the standard output, and reads the results from the standard input. In this case, AutoDock is behaving as an energy server for the alternative search-procedure program.
There are eight recognized commands: AutoDock 's command interpreter is not case sensitive.
"
eval
" Evaluate this state's total energy.
"
epdb
" Evaluate the energy of the named PDBQ file.
"
outc
" Output the last state's PDB-formatted Cartesian coordinates.
"
oute
" Output (non-bond and electrostatic) energy breakdown, by atom.
"
traj
'' Convert an SA trajectory file into PDB-formatted Cartesian coordinates.
"
stop
", "
exit
", "
quit
" Stop the AutoDock command mode interpreter.
Evaluates the total energy of a state defined by the subsequent state variables. This command utilizes the trilinear interpolation routine in
AutoDock
along with the supplied grid maps defined in the parameter file specified after the `
-p
' flag to return this energy. The internal energy of the ligand is also taken into account, as dictated by the values of the torsion angles supplied in the
ntor
lines following this
eval
command line;
ntor
is the number of torsion angles defined in the ligand
PDBQ
file, as described in the section "Defining Torsions in AutoDock". The usage of this command is:
eval <float> <float> <float> <float> <float> <float> <float>
} Tx, Ty, Tz, Qx, Qy, Qz, Qw (in °)
<float>
} ith torsion angle, in °.
:
ntor
lines.
:
where: Tx, Ty, Tz are the coordinates of the center of rotation of the ligand; Qx, Qy, Qz is the unit vector describing the direction of rigid body rotation, about which a rotation of angle Qw degrees will be applied. The following ntor lines hold the torsion angles in degrees, given in the same order as described in the AutoDock log file.
Calculates the energy of the molecule provided in the PDBQ file, thus:
epdb lig.pdbq
where: "
lig.pdbq
" is the
PDBQ
formatted coordinates of a molecule for which the interaction energy with the macromolecule will be returned. The `
-o
' flag supplied at the
AutoDock
execution line specifies the old format of
PDBQ
, with charges in columns 55-61; otherwise it is assumed that the charges are in columns 71-76.
This command is useful when the state variables for a given molecule are not known, e.g. the x-ray crystallographic conformation of the ligand.
Returns the coordinates of the ligand at its current transformed position (in the form of a
PDB
REMARK). The
x
,
y
,
z
coordinates will be determined by the state variables supplied to the
eval
command.
Returns the total internal energy of the ligand and the total energy of the complex, at the current state variables. These two
REMARK
lines are written in
PDB
format, to the command output channel and the log file.
Convert a simulated annealing "
.trj
" file into
PDBQ
format. Usage:
traj lig.trj
where "
lig.trj
" is a simulated annealing (SA) trajectory file written out by an earlier run of
AutoDock
. This trajectory file contains the state variables for the states sampled during a simulated annealing docking simulation. The torsions are assumed to be in exactly the same order as the input ligand
PDBQ
file. The torsion angles in the trajectory file are
relative
to the input ligand's conformation.
See also the Appendix, script "
runtrj
"; and the next section, "Trajectory Files".