Can any one guide me step by step on docking of metal complex (as ligand) using Auto-Dock Vina and Auto Dock 4.2?

01 May 2020 3 9K Report

Respected Scientists and Researchers,

I am a beginner in docking with Autodock vina and Autodock 4.2.

I have heard that it is problematic to carry out docking of metal complexes (as ligand) using Auto Dock Vina and Auto Dock 4.2. Can some body guide be step by step regarding the docking of a metal complex (as ligand) using both Auto Dock Vina and Auto Dock 4.2? What are the possible sources of error and what should be done to execute the docking smoothly?

Thank you in anticipation.

Best Regards,

Arunabh Athreya

Hi Prabuddha Bhattacharya

It would be useful if you would also install autodock tools with your docking software to help prepare your ligand and macromolecules. The quick and dirty tutorials are what I started with when I started with Autodock vina. If I could refer a youtube video, it would be this:

https://youtu.be/ZiuqSzqcD7M

The short description is this:

preparing target macromolecule

Open the protein/DNA/other macromolecule file in Autodock tools GUI

Fix hydrogens and other parameters like charges and tortions (all of this can also be done in UCSF chimera also)

Choose a volume in/on the protein to dock ligands on

Save the .pdbqt file

preparing ligand

Open a ligand file (if you have downloaded a .sdf file, you can just save it as a .mol file on softwares like pymol.) of a valid format like .mol.

In the 'Ligand' menu choose the input as the file you've already opened.

fix hydrogens (I would advise you to start with adding only polar Hydrogens), charges, and check if the torsions are correct.

save the .pdbqt file.

running the pdbqt files on autodock vina/autodock 4: This is fairly easy, for example, run vina with the variables for receptor and ligands as names of your macromolecule and ligand pdbqt files resepctively, and add the values for x, y, and z center values along with their sizes. Alternately, you can write all of this in a config file like this as an example:

receptor = prrotase2.pdbqt

ligand = paba_glum.pdbqt

center_x = -3.75

center_y = -6.636

center_z = -15.749

size_x = 18

size_y = 28

size_z = 18

exhaustiveness = 200

and run vina --config .txt

Hope this helps!

Arunabh Athreya

You are right about that. I had some problems designating charges to Mn3+/Mn2+ centers in a protease. For that I went around and prepped the ligand in chimera using Amber force field. If ADT gives you error while prepping for your metal ions, try this and see if it works better. I think amber and gromos have charge topologies for all 3d elements at least, but you will have to check it out yourself though.

John Peter Mescco

well,

you need the partial charges for you metal complex. Autodock no assign partial charge for metal center. In this case you can search this charge by quantum mechanic methods.

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

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