Format of the the Trajectory Files
The traj command which is used in the trajectory output,
creates trajectories in two formats, one in PDB format which is written
to the log file specified by the -l flag, and one in a
raw ASCII format which is written to the standard output. For example,
if the command issued was:
autodock -p ligand.dpf -l ligand.trj.conv.log -c < trj.conv.com
> ligand.tout
the file ligand.trj.conv.log will contain a PDB formatted
list of all the trajectory steps, while the ligand.tout
file will contain raw ASCII data, with one row for each atom in the ligand,
and each column containing the following data:
-
x-coordinate;
-
y-coordinate;
-
z-coordinate;
-
the intermolecular atomic affinity;
-
the electrostatic interaction energy;
-
the net intermolecular energy (atomic affinity + electrostatic energy);
-
the intramolecular (or internal) interaction energy;
-
the total interaction energy, intermolecular + intramolecular;
-
the annealing temperature;
-
the move code, where
-
1 = immediately accepted because this state's energy was lower than its
predecessor's;
-
2 = probabilistically accepted because although this state's energy was
higher than its predecessor's, the Boltzmann probability criterion was
satisfied at this temperature;
-
3 = rejected because this move hit a grid edge or wall; and
-
4 = rejected because this move's energy was higher than its predecessor's,
and also failed the Boltzmann criterion.
-
the number of the simulated annealing step;
-
the number of the simulated annealing cycle;
-
the number of the simulated annealing run.
Each step in the trajectory is output as single "frame", the order of the
atoms being the same for every frame, which is the order of the atoms in
the input PDBQ file specified by the "move" command in
the ligand.dpf file.
The script "mktrjfld" can be used on the ligand.tout
file to create an AVS field file, extension .fld,
to be read into AVS later by the read field module, thus:
mktrjfld ligand
This requires that ligand.tout already exist, and creates
a file called "ligand.trj.fld".