Dear all, I'm looking for some advice on the rosetta ligand mode.
1)
I am trying both classsic ligand docking and the pose mode. the classic ligand docking works, however, I cannot invoke the pose_ligand_docking function.
here is one example of the command:
./rosetta.gcc aa XXXX X -s XXXX.pdb -dock -ligand -pose -pose_ligand_docking -enable_ligand_aa -ligand_mdlfile XXXX.mdl -dock_mcm -ligand_dock_pert 15 -scorefile XXXXXXX -timer -ex1 -ex2 -nstruct 1 | tee XXXXXX.out
I'd like to set a very strict constraint (certain distance between atoms). But somehow the "-ligand_dock_pert" flag here didn't work, as my ligand was moved far away. I guess that's because it didn't invoke the "pose_ligand_docking" flag.
Hope someone here has some idea. I am really confused.
2)
I also tried to add some .dst file. But I read from previous post that the 2.3.0 version can only handle single .dst input.
If I use the NOE format, then the problem is how do I write the name of two atoms with same type, for example, if both of them have the name "OOC",?
3)
It seems that I need to try the -cst mode. I read some of the documents, finding that not enough information about the single line or complicate mapping format, only two examples with some ambiguous numbers. Where can I find some explanation?
Please help me. Any idea will be appreciated.
Thanks a lot!
-Yizhou