I have taken the example on simultaneous stub placement, and modified it a bit.
In this example, one sidechain is forming a hydrogen bond. I don't need this
part so I removed it from the script. I just need to transplant two hydrophobic hotspots.
The original script works great, but when I modify it, I get problems with
the hotspot constraints. Basically, it seems they are not applied anymore.
The message I get in the output is:
"protocols.hotspot_hashing: Applied 0 hotspot constraints to the pose".
Before this message, the stubs seem top be read without any issues:
"protocols.hotspot_hashing: Read 125 stubs from stubsall.pdb"
Any ideas what could go wrong? I have attached both xml files, the changed one
(placed_simult.txt) and the original example (four_stubs_Oct09_new.txt).