The Molecular Graphics Laboratory Forum

Hi, I want to dock a ligand with my protein and I do have several candidate docking sites in my mind. So I put those docking sites into flexible residues and set the rest into rigid body. However, the docking generated by Autodock 4.2 doesn't take the ligand to interact with the flexible residues. Am I using it wrong? What can I do to achieve the desirable result?

-Zi

Hi ZisAshortName,

I'm very new to ADT, but if your ligand don't dock at the right area, it might be the GridBox. Prove position and size.
Maybe it's a stupid hint, but how I've said, I'm a newby

Just to be sure, docking starts and delivers a conformation, but that con doesn't hit your target site, not?


regards
cis-peptide

What we have done in our lab is to switch what you call your receptor an what you call your ligand. We didn't get what we were looking for but we were successful at docking a small polypeptide with a "receptor".

Remember to allow enough room for your "ligand" to be able to flip in free space.

_________________
TJ Mustard
mustardt(at)onid(dot)orst(dot)edu