At the end of an
AutoDock
job in which more than one run was performed, the program outputs a histogram of clusters and their energies. Look in the
lig.macro.dlg
file for the word `
HISTOGRAM
' all in upper-case. The clustering or
structure binning
of docked conformations is determined by the rms tolerance specified in Å by the "
rmstol
" keyword. The best conformation from each cluster (
i.e.
that with the lowest energy) is written out in PDBQ format at the end of the log file.
Use the UNIX
grep
command to extract information from the docking log file. For example,
% grep "^DPF>" lig.macro.dlg | sed `s/^DPF> //'
would extract all the lines that begin with "
DPF>
", and pipe them into the stream editor, "
sed
", to strip out the "
DPF>
" prompts. Since each line read in from the input DPF is echoed in the log file on such lines, this UNIX command would recover the original DPF that was used to generate "
lig.macro.dlg
".
To extract the conformations from the docking log file just use the "
dockedtopdb
" command:
% dockedtopdb lig.macro.dlg > lig.macro.dlg.pdb
This writes out a PDB formatted file, and uses the `
MODEL
' and `
ENDMDL
' records to denote the different dockings. Check that your molecular modelling package or viewer can parse these PDB records.
Or if you need a PDBQ formatted file, use "
dockedtopdbq
" thus:
% dockedtopdbq lig.macro.dlg > lig.macro.dlg.pdbq
These docked structures can be read into any appropriate molecular modeling program, and the results compared, where possible, with the experimental data.
The table of ranked clusters , under the heading `CLUSTERING HISTOGRAM' in the log file, shows the final docked energy for each conformation, and the rms difference in Å between the lowest energy member of the cluster and every other member. The rms for the lowest member of the group is by definition zero. You can extract this clustering histogram very easily using this command, which will print the results to the terminal:
% gethis lig.macro.dlg
After this table in the `
lig.macro.dlg
' log file, the docked structures are output in PDBQ format. Each conformation has a set of REMARK records, one of which describes the rms difference between itself and the coordinates specified in the original input PDBQ file.This can be useful for comparing how close each docked conformation is to the experimentally determined position.