Question

If there is h bond but docking energy is positive what dose it mean

Answer 1

Answer:

Explanation:

I needed clarification regarding the binding energy significance in docking studies. I am currently docking a polysaccharide with a target and getting a positive binding energy.

I am really perplexed as to why  this might be happening. Also it is normal to have a positive binding energy and get hydrogen bond formation??

I am using Autodock tool to perform docking.

Answer 2

Explanation:

energy values given by docking algorithms have little correlation with true binding affinities. At best, you can use these energies to rank the different resulting poses of a docking run with the same ligand and protein. Still, I would not trust these values even for ranking and I would visually inspect the all resulting poses to see if the putative binding pose proposed makes sense.