How to run DOCK with a focusing term (internal energy) included

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Using DOCK with a focusing term (internal energy)

To use DOCK3.6 with a focusing term, you first need to prepare the small molecules for docking. The current DOCK3.6 program does not support that energies are specified per-conformation, so the code has been modified to dock each conformation separately to circumvent this feature.

Step 1: Prepare database of molecules from smiles.

The first part involves preparing the databases and is based on Michael Mysinger’s To prepare a series of molecules for docking (smiles in test.smi), run the following 4 commands on sgehead:

set dudI = /raid7/people/jens/internal_energy/code/code_mmff.min_amsol_hflip/dbmake
set INTE13 = /raid7/people/jens/internal_energy/code/code_mmff.min_amsol_hflip
set baseI = /raid7/people/jens/internal_energy/code/base
$dudI/ -i test.smi will prepare the molecules on the cluster. Preparing the molecules for docking with focusing requires considerably more computation time than, so be prepared to wait a bit longer.

Step 2: Run docking with modified DOCK code

The generated databases cannot be run with the current version of DOCK3.6. Instead, use a modified executable:




One line has to be added to your INDOCK file in order to switch on focusing (internal energy):

scale_focusing                1.0

Step 3: Analysis of results

The results can be combined with the standard DOCK analysis tools, e.g.

If you have any problems or would like to know more about how the databases are prepared, don't hesitate to contact me!!!

Jens Carlsson