Not to overwhelm the forum but I was wondering if anyone else has run into the following problem when using -dock_pert:
I am successfully able to use the "local refinement" procedure to generate decoys with small perturbations compared to my input structures and everything works great. I can do this by running docking_protocol.linuxgccrelease @flags where flags contains:
Wanting to increase the search space, I thought to use -dock_pert to add a larger perturbation. I used the same input structures and identical flags as above but substituted "-docking:dock_pert 3 8" instead of "-docking:docking_local_refine".
The decoys produced by doing this appear to have translated the ligand about 500 angstroms away from the receptor. The center of mass distance between the original placement of the ligand in my input structure versus the resulting decoys ranges from about 491 to 505 angstroms. I would also like to add that the problem seems to be in translation perpendicular or normal to the ligand/receptor interface (ie the decoy ligand protein structures form a nice cluster with structures having nice small perturbations relative to each other...only that the cluster is ~500 angstroms away from my original receptor/ligand interface).
Perhaps I'm missing some other necessary flags which support -dock_pert 3 8?
I tried specifying -dock_pert 3 8 8 but it does not accept the third argument. I also tried adding -dock_mcm but it does not recognize that flag. Any thoughts?