rhuey at rhuey at
Wed May 21 10:08:53 PDT 2008


(1) clusters the results from all of the docking
logs in a  directory. It then builds an output string based on the options
with which it is invoked.

Here it is outputting information about the largest cluster in that
clustering. Note that this is not necessarily the cluster containing the
lowest overall energy.

Here are the meanings of this set of column headings:

largestCl_dlgfn: filename of the dlg file which contains the result with
the lowest energy in the largest cluster.

#runs: total number of runs found in all the dlg files in the specified

#cl: number of distinct clusters formed in the clustering done on all the
dlg files in the specified directory

LE_LC: the energy of the lowest energy conformation in the largest cluster

rmsd_LC: the rmsd difference between the lowest energy conformation in the
largest cluster and the reference ligand conformation. This is the input
ligand conformation unless a different reference is specified with the
'-f' flag

#ats:  number of atoms in the ligand

#tors: number of active torsions in the ligand

(2) the format for the output of floating point numbers rounds to 4
decimal places.


> Dear autodock list,
> I have just used the script as per the tutorial
> "Using AutoDock 4 for Virtual Screening"
> The top of my file reads:
> largestCl_dlgfn    #runs #cl #LC    LE_LC     rmsd_LC #ats #tors
> ZINC00000077_rigid/ZINC00000077_rigid, 20, 14,  3, -6.0700, 56.6501,
> 25, 6
> ZINC00000123_rigid/ZINC00000123_rigid, 20,  4,  8, -5.7200, 51.5977,
> 25, 1
> I have two questions:
> 1. Could someone tell me what the abbreviations in the column titles
> stand for?
> 2. When I look through the specific docking logs I cannot actually
> find these values. For instance when I do a text search for -6.0700 in
> the log file corresponding to the first ligand I cannot find the
> value. How exactly does calculate these?
> Thanks!
> Simon
> ________________________________________________
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