How to automate docking setup and screening?

[Andrew Orry]

Q. How to automate docking setup and screening?

A.

You can automate docking setup for each pdb using _dockBatch.

$ICMHOME/icm64 $ICMHOME/_dockBatch 1xbb.pdb ligmol=asti

In ligmol= option one can provide either molecule name within .pdb or a separate .mol or .mol2 file which should be used to define binding site.

If ligand is within .pdb and ligmol=ligmolname it will be removed during setup.

optional - you can run screening automatically by defining the sdf file at the end after ligmol but in your case you need to run on the cluster so see _dockScan information below

e.g.

$ICMHOME/icm64 $ICMHOME/_dockBatch 1xbb.pdb ligmol=asti chem_database.sdf

After setup you should see files called D_PDBName which contain the receptor and docking maps.

e.g. for 1xbb

-rw------- 1 andy Molsoft   1227 Dec  4 15:38 D_1XBB_probe.ob
-rw------- 1 andy Molsoft 587192 Dec  4 15:38 D_1XBB_rec.ob
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_gh.map
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_gc.map
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_gl.map
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_ge.map
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_gb.map
-rw------- 1 andy Molsoft 626424 Dec  4 15:38 D_1XBB_gs.map
-rw------- 1 andy Molsoft   2568 Dec  4 15:38 D_1XBB.dtb
-rw------- 1 andy Molsoft   2691 Dec  4 15:38 D_1XBB_LOG.htm

To run the docking without _dockBatch  use _dockScan

http://www.molsoft.com/man/ligand-fit.html#dockScan

Please let me know if you have any questions - we could setup a webex if you have any specific question and I can see your screen.

Best regards,

Andy

[Andrew Orry]

Q. How to define the pocket using residue numbers rather than the ligand in _dockBatch

If you are going to select by pocketResidues first you must delete the ligand first. 

Then use pocket=a_/then_the_residue_numbers_around_the_pocket

e.g.

$ICMHOME/icm64 $ICMHOME/_dockBatch 1xbb.pdb pocket=377,402,385

If you have run ICMPocketFInder the pockets are labeled g_pocket...

To select neighboring residues to a pocket use something like this 

# e.g 5.0 angstroms around pocket called g_pocket_1xbb1

PocketResidues=Sphere(g_pocket_1xbb1 5.0)

then use String(selection) to convert a selection into text form http://www.molsoft.com/man/icm-functions.html#String-selection

e.g.

l_showResCodeInSelection =no
String(Res(PocketResidues))