BKS lab Structure preparation

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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 takes as input a mol2 file with very strict mol2 naming

You will need to have Ligand pdb file ( LZ6.pdb )

isssue the following command:

 file2file.py LZ6.pdb LZ6.mol2 

the script file2file.py 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.

If you want to score a native ligand you should first convert it to test.eel1 using file2file.py 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!!!

To generate the necesary cofactor parameter file issue the following command:

 $mud/charge_cofactor.csh LZ6.mol2 LZ6
 charge_cofactor.csh LZ6.mol2 LZ6 hydrogens

by adding the word "hydrogens" the end of the command the hydrogens will also be included in the

the output of this command 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


first run make with out 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.

If you have confidence in your preporation then you can add the prot.table to the libary:


This will allow others to uses this preperation with the automated scripts.

perparing ligands for docking