DOCK 3.7 tart: Difference between revisions
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** 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/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 | ** Edit RSK2-tart/amb.crg.oxt to reflect the same changes | ||
**Note that the prot.table.ambcrg.ambH and amb.crg.oxt are '''not''' in working. they must be outside the working dirtory, the scripted blastermaster will copy them. | |||
* 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: | * 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 | ** $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=/path/to/RSK2-tart/amb.crg.oxt --vdwprottable=/path/to/RSK2-art/prot.table.ambcrg.ambH | ||
Revision as of 16:28, 20 September 2016
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.pdb 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
- Note that the prot.table.ambcrg.ambH and amb.crg.oxt are not in working. they must be outside the working dirtory, the scripted blastermaster will copy them.
- 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.
You may want to visualize your modified potential maps. See the following page on how to do this with pymol: