The Molecular Graphics Laboratory Forum

Hello,

I haven't been using AutoDock for very long, but been keen to learn and read several publications as well as all the tutorials available online (I did them too, to make sure I grasp the theory). And it was all fine, until I try to dock my own ligands into my protein. Docking explosives into pOBP ( pdb code: 1E02 - its a dimer, so I remove one chain as well as ligands which are inside the "active site". All waters are removed as well). When I only try to use the program to dock the ligand into rigid protein, its all fine (the Binding Energy looks acceptable) but when I try to dock the ligands into flexible protein, my Binding Energy goes to values like 4x10^6 kcal/mol.
I have followed the tutorial which I've found on the Scripps website, yet it doesn't seem to work for me.. It seems as if the rigid file which I save during defining the flexible residues, also contains flexible residues and the flexible atoms are colliding, causing extreme energies...

Any ideas how can I fix it?

All help would be appreciated.

munieq11