Hi all
Recently I'm now doing large scale protein ligand docking using rosetta
while I'm doing , I got the following warning not error
This should never happen after extending the interface
protocols.ligand_docking.ligand_options.MinimizeBackbone: (6) [ WARNING ] for backbone minimization to work properly, a stretch of at least 4 residues needs to be allowed to move. Stretch between 298 and 299 is too short. This should never happen after extending the interface
protocols.ligand_docking.ligand_options.MinimizeBackbone: (6) [ WARNING ] for backbone minimization to work properly, a stretch of at least 4 residues needs to be allowed to move. Stretch between 298 and 299 is too short. This should never happen after extending the interface
The program seems to get stucked in loop and continuously print this warning , never ending
I suspect the input might have a problem, but I can not figure out
Attached are my input file
Any kind of suggestion would be welcomed
Thanks
| Attachment | Size |
|---|---|
 crystal_complex.pdb | 212.69 KB |
It's the chainbreak between R309 and M312 (the residue numbers being printed are "pose numbers", where the first residue is 1 and each residue increments by one, regardless of chain.) -- Rosetta is trying to set up flexible backbones in that region, and can't properly set up the movement. This is also complicated by the fact that R309 is missing its carbonyl atoms in the file, and thus is being discarded by Rosetta.
One option is to fill in the loop with the missing residues. The Protein-protein docking tutorial from https://meilerlab.org/rosetta-workshop-2023/ gives a relatively simple protocol. For that protocol to work, you need to have all the residues present, but they don't necessarily need to have decent coordinates (Rosetta should rebuild things, so long as you set the loop file to do so.) I was able to mock something up by just copy and pasting from other residues in the file and then editing the residue numbers. Your loop file would be something like `LOOP 299 303 0 0 1`, (again, pose numbering) though you could extend a bit on either side to give a bit more flexibility in loop closure.
The other option is to tell Rosetta to treat things like two separate chains. That will introduce a protonated nitrogen and a oxygenated carboxylate in the gap, as well as permitting slightly more flexibiliity than you may want to those ends. But it's easy -- just add a TER line to the input PDB between the R309 and M312 residues. (And delete the R309, as Rosetta will do that anyway.)