As part of workflow - Alicecomma/VinaCarbResults GitHub Wiki

Here a write-up of an overall workflow.

1. Create a new folder, e.g. /Flavans:

   3klk.enzyme
   /3klk/
   /Flavans
   

2. Find chemical reference drawing, e.g. Apigenin.

3. Draw in Avogadro. Alternative 3D structure software exists.

4. Save as /Flavans/Apigenin.pdb:

   3klk.enzyme
   /3klk/
   /Flavans
   /Flavans/Apigenin.pdb
   

5. Open Apigenin.pdb with a text editor, e.g Programmer's Notepad.

6. Add appropriate oxygen names, e.g in-ring O1, ketone O4 and then three alcohols O4' (phenol-like), O5 (near ketone) and O7 (far from ketone). This is easiest while Avogadro is open to View > Properties (Alt-V,P) > Atom Properties .. and select the oxygens to see their location. Compare to a known numbering system, say this one.

7. Save Apigenin.pdb.

8. Generate Apigenin.pdbqt. I automate .pdbqt generation by calling prepare_ligand4.py from MGLTools like cmd /c python.exe prepare_ligand4.py -l Flavans/Apigenin.pdb -o Flavans/Apigenin.pdbqt -v. This requires:

   python.exe
   prepare_ligand4.py
   /Flavans
   /Flavans/Apigenin.pdb
   

9. Download the enzyme (e.g PDB: 3KLK):

   /3klk/
   /3klk/3klk.pdb
   

10. Prepare the enzyme using MGLTools:

    /3klk/
    /3klk/3klk.pdb
    /3klk/3klk.pdbqt
    

11. Run VinaCarb or AutoDock Vina with appropriate position parameters like --enzyme [1]/[1].pdbqt --ligand [0]/[2].pdbqt --out [0]/[2]/[1].pdbqt --log [0]/[2]/[1].log. Other parameters have to be included as usual. Extra parameters could be, say, --num_modes 120 --exhaustiveness 20 --energy_range 10 for VinaCarb.

    3klk.enzyme
    /3klk/
    /Flavans
    /Flavans/Apigenin.pdb
    /Flavans/Apigenin.pdbqt
    /Flavans/Apigenin/3klk.log
    /Flavans/Apigenin/3klk.pdbqt
    

12. If AutoDock Vina is run repeatedly, postfix filenames to be of the form [1]_2.log, [1]_3.log, [1]_4.log.

    3klk.enzyme
    /3klk/
    /Flavans
    /Flavans/Apigenin.pdb
    /Flavans/Apigenin.pdbqt
    /Flavans/Apigenin/3klk.log
    /Flavans/Apigenin/3klk.pdbqt
    /Flavans/Apigenin/3klk_2.log
    /Flavans/Apigenin/3klk_2.pdbqt
    /Flavans/Apigenin/3klk_3.log
    /Flavans/Apigenin/3klk_3.pdbqt
    

13. Run VinaCarbResults [0] [1] [2], e.g VinaCarbResults Flavans 3klk Apigenin

    3klk.enzyme
    /3klk/
    /Flavans
    /Flavans/Apigenin.pdb
    /Flavans/Apigenin.pdbqt
    /Flavans/Apigenin/_3klk.pdb
    /Flavans/Apigenin/_all.tsv
    /Flavans/Apigenin/_best.tsv
    /Flavans/Apigenin/3klk.log
    /Flavans/Apigenin/3klk.pdbqt
    /Flavans/Apigenin/3klk_2.log
    /Flavans/Apigenin/3klk_2.pdbqt
    /Flavans/Apigenin/3klk_3.log
    /Flavans/Apigenin/3klk_3.pdbqt
    

14. Open _best.tsv. The file can be imported immediately into Excel and contains information about best binding modes of each oxygen.

    	UNL(1)	UNL(1)	UNL(1)	UNL(1)	UNL(1)
    	O1(10)	O4(11)	O4'(18)	O5(20)	O7(22)
    
    3klkG		-6.6	-6	-6.8	-6.8	kcal/mol
    		33	66	11	10	mode
    		1	1	1	1	run
    

15. Open _all.tsv to check all binding modes where an oxygen is present in the active site -- not just the best modes.

    Enzyme	Label	Name	Run	Mode	VC	AV
    	(nr)	(id)	nr	nr	kcal/mol
    
    3klkG	UNL(1)	O7(22)	1	10	-6.8
    	UNL(1)	O5(20)	1	11	-6.8
    	UNL(1)	O7(22)	1	23	-6.6
    	UNL(1)	O7(22)	1	30	-6.6
    	UNL(1)	O4(11)	1	33	-6.6
    	UNL(1)	O5(20)	1	34	-6.6
    	UNL(1)	O7(22)	1	35	-6.6
    	UNL(1)	O7(22)	1	38	-6.5
    	UNL(1)	O7(22)	1	47	-6.3
    	UNL(1)	O4'(18)	1	66	-6
    	UNL(1)	O7(22)	1	79	-5.7
    	UNL(1)	O4'(18)	1	93	-5.2
    

16. Open _3klk.pdb using Pymol to see each of the best binding modes (in _best.tsv).