Output

dock reports several kinds of information as output which is either written to screen in interactive mode or written to file in batch mode. Each section of the output is discussed below.

Heading

UUUUUUUUU CCCCCCC SSSSSSS FF/ FFF/

UU/ UU/ CC/ CC/ SS/ SS/ FF/ FFF/

UU/ UU/ CC/ CC/ SS/ FFFFF/

UU/ UU/ CC/ CC/ SS/ FF/ FF\

UU/ UU/ CC/ CC/ SS/ SS/ FF/ FF\

UUUUUUUUU/ CCCCCCC/ SSSSSSS/ FF/ FF\

University of California at San Francisco, DOCK 4.0

__________________Job_Information_________________

launch_time Wed Mar 19 12:05:01 1997

host_name mycomputer

memory_limit 126062592

working_directory /usr/people/user

user_name user

The heading lists general information about the current job. The launch_time, host_name and working_directory fields are useful to help the user archive the run conditions. The memory_limit field refers to the amount of RAM in bytes available to the job. This is can at most be equal to the physical memory of the computer, but may be less if limits have been imposed on the users shell. If the job requires more RAM than is available, then execution is stopped and an error message is reported.

Parameters

________________General_Parameters________________

flexible_ligand no

orient_ligand no

multiple_ligands yes

score_ligand no

chemical_screen no

parallel_jobs no

____________Multiple_Ligand_Parameters____________

ligands_maximum <infinity>

initial_skip 0

interval_skip 0

____________________File_Input____________________

ligand_atom_file old.mol2

____________________File_Output___________________

ligand_none_file new.pdb

All input parameters are echoed into the output. In fact, the output file may be used as an input file for another run. This is a useful technique to clean up an old, cluttered input file and make a tidy, well-organized input file.

This particular parameter list is nearly the shortest possible since most general parameters have been turned off. It is constructed automatically when dock is used to convert a molecule file format (see Molecule File Conversion on page 54 ).

If a parameter is not needed it is not reported in the output. The user can override this feature and force all parameters to be written out by using the -v flag (see Command-line Arguments on page 53 ).

Results

_________________________Docking_Results_______________________

Name : ligand1

Description : ****

Orientations tried : 616

Orientations scored : 500

Best energy score : -59.02

Intramolecular energy score : 12.18

Intermolecular energy score : -71.20

RMSD of best energy scorer (A) : 2.39

Elapsed cpu time (sec) : 492.87

The docking results of each molecule are output as above. In terse mode (-t flag) all results are printed on a single line.

This particular output is from the flexible docking of a molecule.

Performance

______________________Docking_Performance______________________

Procedure timings time (s) percent

Screen 0.00 0

Orientation Search 0.48 0

Orientation Score 49.90 10

Conformation Anchor 0.05 0

Conformation Peripheral 442.38 90

Other 0.02 0

Total 492.94 100

Minimizer usage minimum average maximum

Calls per molecule 4200 4200 4200

Score improvement per call 0 2.7e+10 8.7e+13

Vertices per call 1 3 6

Cycles per call 1 2 5

Iterations per cycle 1 15 100

This section of the output is generated if the user used the -p command-line flag (see Command-line Arguments on page 53 ). It is intended to help the user to understand the performance bottlenecks of a particular run and to make informed parameter choices. Since minimization can consume significant portions of cpu time, it is profiled in more detail.

This particular output is from a flexible docking run in which a majority of the cpu time is spent during the peripheral conformation search.