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

The co-factor needs to be in the rec.pdb and rec.crg. The cofactor should be included as part of the receptors and needs parameters so that Electrostatic, Solvation, VDW grids can be calculated. To calculate the VDW types and charges call the following scripts:

The script "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 ). This file should have hydrogen.

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.

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 preparation then you can add the prot.table to the library:


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

perparing ligands for docking