BKS lab Structure preparation

Perparing receptors for docking with DOCK 3 is largely automated using the DOCK Blaster pipeline. However there are some things that may still require manual intervention.

Preparing cofactors or nonstandard residue for receptor

In order to include a cofactor (or nonstandard residue) as part of the receptor, we sould Adding a cofactor to DOCK

first you need the co-factor to be in the rec.pdb (Actually the rec.crg) so that solvation could be calculated on it. To take care of VDW typing and charges there's a scripts called:

$mud/charge_cofactor.csh that gets as input a mol2 file with very strict mol2 naming

so if you have a LIG.pdb

first do:

 file2file.py LZ6.pdb LZ6.mol2 

(file2file is an addon to convert.py (which is supplied by open eye) that is A more stringent on keeping original atom names, and B the only script able to convert to and from test.eel1 format - so if you want to score a native ligand you have to first convert it to test.eel1 using this scripts and than you can use doscoreopt.sh on it!)

following conversion - check atom types with Chimera to see they are accurate and especially MAKE SURE PROTONATION STATE IS CORRECT GOING INTO THIS SCRIPT!!!

the output of

 $mud/charge_cofactor.csh LZ6.mol2 LZ6

is LZ6.prot.table

which you should add the the prot.table in grids and then run:

 $mud/prot2crg.py < prot.table.ambcrg.ambH >! amb.crg.oxt

Then:

first run make w/o the co-factor, you can kill it when it starts solvation calculations

modify the prot.table and create amb and now you can also add the coordinates directly to rec.crg - do this and re-make.