Hello everyone,

I am conducting molecular docking using Autodock Vina. The receptor (protein) is huge therefore the grid spacing 0.375 A is not enough (Autodock Tools). So, I also increased the spacing to cover the whole protein (blind docking). Now, I have two sets of values for grid box one for 0.570A and another one for 1.0A.

I run the docking using Autodock Vina without specify grid spacing either in the configuration file or in the command (because it gives error if I added information regarding grid spacing). The results of autodock vina is different for these two sets of values. For grid spacing 1.0A, the binding energy is positive 1080 kcal/mol. But for grid spacing 0.570A, the binding energy is negative -18.8 kcal/mol.

Questions:

1. What is the default grid spacing for Autodock vina? is it 0.375A or 1.0A?

2. How to specify the grid spacing other than 0.375A in Autockdock Vina?

3. Any suggestions for blind docking using autodock vina (but the protein is big and the default spacing is not enough).