Note : Trajectories can only be generated during a simulated annealing run: they are not available for the population-based genetic algorithm methods.
A trajectory (of state variables) can be written out during a normal simulated annealing docking , if the trajectory-frequency (set by the keyword "
trjfrq
") in the docking parameter file is greater than zero. This value defines the output frequency, in steps, for states sampled during the run. The default trajectory filename extension is "
.trj
" . These
state variables
are all that is needed to regenerate the coordinates of the ligand. The trajectory control parameter (either "A" or "E") allows the user to record only
accepted
moves (A); or, moves which are
either
accepted or rejected (E). Just for information, a sample "
.trj
" trajectory file is shown below; you will not need to create such files (unless you feel like creating an animation!):
______________________________________________________________________________
ntorsions 2
run 1
cycle 1
temp 300.000000
state 1 A -3.745762 -1.432243 -9.518171 23.713793 23.076145 0.713534 -0.023818 0.700216 30.606248
-4.894825
2.661499
:
:
state 6 R -12.679995 -1.452641 -9.259430 21.634645 23.135242 0.653369 -0.440832 0.615448 39.127316
-31.636299
10.261519
state 7 a -8.746072 -1.458231 -9.080998 21.356874 23.325665 0.648312 -0.448577 0.615200 41.075955
-37.935175
11.918847
:
______________________________________________________________________________
There are several keywords: "
run
" and "
cycle
" are self-explanatory; "
ntorsions
" is the total number of changing torsions in the ligand; "
temp
" is the annealing temperature for all subsequent entries, unless otherwise stated. Each "state" record has the format:
state nstep acc_rej_code e_total e_internal x y z qx qy qz qw
where:
nstep
= the number of the step, within this cycle;
acc_rej_code
= `
A
' = an accepted move whose energy was
lower
than its previous state;
= `
a
' = an accepted move whose energy was
higher
than its previous
state, which nevertheless passed the
Monte Carlo
probability test at
this temperature;
= `
R
' = a rejected move.
= `
e
' = an edge-hit, also a treated as a rejected move.
e_total
= total energy of the system, ligand + macromolecule;
e_internal
= internal energy of ligand only;
x,y,z
= translation of ligand center;
qx,qy,qz,qw
= quaternion, which describes the ligand's orientation;
In order to get a coordinate-based trajectory file, for visualization, the command mode of
AutoDock
must be used to regenerate the coordinates from the state variables. Use the "
traj
" command with the name of the pre-calculated trajectory file. For example, suppose there is a command file called "
trj.conv.com
" that contains:
_____________________________________________________________________________
traj lig.trj
stop
_____________________________________________________________________________
AutoDock would be executed a second time using the following command,
% autodock3 -p lig.macro.dpf -l lig.macro.trj.conv.log -c < trj.conv.com > trj.conv.out