I am new to rosetta and I want to perform protein-lignad docking using rosetta3.13, I used my own PDB files and the option.txt, dock.xml under the folder rosetta/main/demos/tutorials/ligand_docking to perform docking. I found the ligand was still outside the protein after docking. Therefore, I tried to add the start coordinates for the ligand in the dock.xml but didn't find a right way. Could you help me with this? I attached the PDB file I used for docking.
The easiest, most basic, yet crude way to put a ligand roughly where you want it is by moving it there by hand in PyMOL.
Opening your PDB in PyMOL with the ligand as a different object (`create ligand, resn XXX`, `remove resn XXX and not ligand`) and then click on the right hand side panel where it says "Mouse mode" in hacker green, until it switches to 3 button editing. Then find your ligand (`zoom ligand`) and click and drag with Shift+middle button (Move Object).
To put everything back together, `create combo, ligand and whateveryourproteiniscalled`. `save out.pdb, combo`.
Thank you for your reply! The problem is I have a large number of ligands perform docking. It might be a problem to do this manually. Is there any way to do this by code in rosetta? Like, add the coordinates in the dock.xml?
I have never used that script, but I was the first to comment so I'll throw in my two pence. So hopefully someone will correct me here!
The placement mover in ligand_dock.xml is StartFrom, followed by SlideTogether.
I had not used these (as I don;t use scripts) and SlideTogether seems interesting, so I gave it a go but in PyRosetta (as it is quicker for me with copypasted code) to see if I could see a similar issue. I loaded 1UBQ added a calcium and set it to start from the first atom of the first residue.
SlideTogether seems to do its thing, but the starting location was bad.
The StartFrom does the weird stale thing in PyRosetta, but simply scoring the pose fixes it... I assume it is fine in Rosetta XML, but the location is not right.
Applying it multiple times, shifts it for me farther and farther of the same amount.
You might want to check the result of that mover alone...
But a hack could be to simply have your active site at the origin and skip the StartFrom...