There is no need to do conformational search for ligands before a docking study. A quick energy minimization would be enough. Almost every docking method performs its own kind of conformational search for a ligand in the binding pocket.

Oh Great thanks for your reply. It really saved lot of my time.

Vicky

Just as mentioned, every docking program is able to produce conformers "on the fly". However in some cases, potential results may benefit from a high number of input conformations. My advice would be to increase the number of initial conformers that MOE uses for docking, this has little effect on calculation times as the most exhaustive part is scoring.

Regards

I am guess you are talking about the London GB and GBV/WSA scoring functions.These are my settings

London GB - 30

GBV/WSA - 20

do you think I should increase or decrease these numbers.

Thanks again,

Vicky

There should be a couple of buttons with a gear icon on them. Pick the one on the left side to London dG, a small panel should pop up, there you can increase the number of placements for scoring.

The numbers you mentioned are the "final poses" MOE should take. For example if you ask for 5000 placements this yields 30 poses with top score using London dG followed by rescoring with GBVI/WSA for only 20 of them. Thus, you end up with 20 poses on the mdb file.

As I said the placement and first scoring are rather quick, I would suggest to use around 50-100 and 5-10 poses respectively.

Regards

Oh OK Got it thanks. really appreciate your reply.

Vicky

I tried docking of some of the ligands with GOLD software but the result with the higher number of conformations always gave higher docking scores VS. with a single minimized structure. In my opinion, if the ligand is rigid and not much flexible, just single minimized structure is enough. But if the ligand is highly flexible, it is better to dock with multi number of conformations.