INDOCK,
which contains the input parameters. Since some of the parameters will be
different for each run, a directory should be created to contain each INDOCK
and probably the corresponding output. Using a separate directory is a good
idea even for just one run.
Keywords available for
The input and output parameters are relevant to all DOCK runs.
The matching parameters determine how many different ligand orientations DOCK
will examine - these parameters are relevant to all DOCK runs.
Increasing or decreasing the number of orientations increases or
decreases the amount of computer time used by DOCK and the disk space used by
single-mode runs. It may take some experimentation with these parameters to
discover what works best for a particular system. Be cautious when increasing
bin sizes and bin overlaps; small changes can produce large increases in the
number of orientations generated.
When running SINGLE mode to generate many orientations for one molecule,
one uses these parameters.
When running SEARCH mode to obtain the best orientation for each of many molecules in a database,
one uses these parameters.
Which scoring parameters to use depends on the scoring option chosen.
The chemical matching parameters are used to specify how labeled spheres and
atoms (if any are used) are to be matched. Leave them out if you do not use
chemical matching.
Parameters for force field score optimization (minimization) of orientations
are listed here. Minimization varies the position of ligands in order to
find orientations with improved force field scores.
Consult the reference manual for a for a description of how to use minimization.
It lists the relevant
Start DOCK from the directory you created for
During a SEARCH run (which can take anywhere from hours to days to weeks to
finish), you can follow DOCK's progress through the database by
looking at the last few lines of
Extended PDB format allows more information to be included in the atom
records. Scores for options not used originally may be quickly evaluated for
ligand files with this format using scoreopt or scoreopt2.
However, some molecular display programs may not accept this format. If you
find that you cannot display your ligands, you can convert them to PDB format
using the program x2pdb supplied with DOCK. A useful way to view
ligands is to display the surface of the protein active site along with a few
important residues, then examine ligands one at a time. showesp may be
used to visualize the electrostatic potential due to the protein, and
showprobe can display the interaction energy of a probe with the force
field grid. splitmol can be used to separate ligand orientations into
individual files if necessary.
Creating
Parameters in the INDOCKINDOCK file are specified by keywords, which are listed one
to a line. The desired value of each parameter follows the keyword on the same
line. You may create the INDOCK file with a text editor or copy one of the
examples supplied with DOCK and modify it to suit your needs. The reference
manual includes several sample INDOCK files. You only need to include in your
INDOCK file those parameters relevant to your calculation or variables whose
values you want to change from their defaults. Any line beginning with # will
be considered a comment and ignored; comments can be quite useful in making the
file more understandable.INDOCK are listed here. The values suggested are
reasonable initial guesses; they may not be the best values for your particular
system. We suggest that you experiment with them to see what works best for
you.distmap_file should be included for any option involving contact scoring
(contact, contact+delphi, contact+forcefield).
Delphi_file is used only
for contact+delphi. The remaining parameters in this table pertain to force
field scoring and are used with the contact+forcefield or forcefield options.INDOCK keywords and gives guidelines for choosing parameter values.
Starting a DOCK Run
Before running DOCK it is a good idea to check whether there are other jobs
running on the same machine. DOCK runs use substantial amounts of CPU time;
consider any other users sharing your computers when deciding whether to start
more than one run at a time. Be aware of any policies your site has regarding
cpu time used.INDOCK. Check a few minutes
after you start the run to be sure that it is still going; if it has stopped,
look for mistakes in the input. Beginners should check disk usage occasionally
while the job is running, just in case the program is creating incredibly large
files which might overflow the available space.OUTDOCK. The number preceding the last
nathvy tells approximately how many ligands have been examined.
Restarting a Search Run
In SEARCH mode, DOCK periodically saves in the output file the information
necessary to restart the search from its current location in the database. If
there is a power failure or the system crashes, you can set up a new run to
start where the last one was stopped. First, you must rename OUTDOCK, since
DOCK will try to create a new OUTDOCK file, and it cannot do so if one already
exists. Then set the restart parameter in INDOCK to yes and start the job
again. (Do not change the remaining files, since DOCK needs them to restart
successfully.) When the restarted run finishes, the sorted list of ligands in
the output file will include the top scorers from the entire database. However,
some of the statistics in OUTDOCK will refer to just those ligands examined in
the restarted run - see the reference manual for details.
Looking at the Results
DOCK puts its output in the directory it was started from, that is, where the
INDOCK file is. For SINGLE runs, there is one file of orientations per sphere
center; the names of these files are outfil+the cluster number. For
search runs, there are files containing top-scoring ligands for each type of
scoring chosen. Ligands with the highest contact scores are in a file named
outfil+the cluster number, top electrostatic ligands are in a file named
outfil+eel+the cluster number, and the file of ligands with the best
force field scores is called outfil+ff+the cluster number. The ligand
files are in extended PDB format, which differs from PDB format in the columns
to the right of the coordinates in the ATOM records. Each orientation or ligand
in the file has a separate residue number. The scores are given in the REMARK
records at the beginning of each residue and are also listed near the end of
OUTDOCK.
Curator: Daniel Gschwend, gschwend@cgl.ucsf.edu (rev. 1 September 1995)
Are there standard bin sizes?