DOCK 3.7 tart

Tarting refers to the polarization of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generally one would redefine the partial charges distribution of a specific amino acid, and then use this modified residue when calculating the electrostatic potential for the receptor. Below is a step by step example:

• Let's say you ran docking against RSK2, so you have a docking directory that looks like: rec.pdb, xtal-lig.pdb, dockfiles, working, INDOCK
• Make a new dir e.g. RSK2-tart, and copy some input files into it:
  • mkdir RSK2-tart
  • cp RSK2/rec.crg RSK2/xtal-lig.pdb RSK2-tart
  • mkdir -p RSK2-tart/working
  • cp RSK2/working/rec.crg.pdb RSK2-tart/working
  • cp RSK2/working/prot.table.ambcrg.ambH RSK2/working/amb.crg.oxt RSK2-tart
• Now edit the files to represent your tweaked polarization. Let's say we want to polarize the backbone of MET496 (In this case the kinase hinge region) by +-0.4
  • Edit RSK2-tart/working/rec.crg.pdb to rename "MET A 496" to "MEU A 496"
  • Edit RSK2-tart/prot.table.ambcrg.ambH to add a MEU amino acid. You can copy the block for MET and rename it to MEU, to polarize the backbone, change the partial charge of the backbone amide proton by +0.4 (i.e. "H MEU 0.648" instead of "H MEU 0.248") lower the backbone carbonyl oxygen by the same quantity ("O MEU -0.500" to "O MEU -0.900")
  • Edit RSK2-tart/amb.crg.oxt to reflect the same changes
• Now all that's left is to run the protein preparation script (blastermaster.py) with the modified parameter files, and without re-protonating the protein:
  • $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-art/prot.table.ambcrg.ambH

When the preparation is done, your protein should be "Tarted". You can proceed to docking.