LIGAND APPEARS TO BE DOCKED INTO EMPTY SPACE

Please look at what I posted at https://www.rosettacommons.org/node/9554

Another idea is that you are only displaying the backbone of your protein.

If you show the sidechains and all the hydrogens, maybe the docking contacts will be more apparent.

I hope that helps!

Hi Gabe,

In DOCKING_IMAGE3.png above, is the ligand on the left and rendered with X’s while the protein is on the right?

I have never used the ligand_docking protocol, but I have used the docking2 and symmetric_docking protocols. My sense is that the docking protocols are fairly sensitive to the initial positions and conformations you give it. If you rearrange the objects you want to dock and then do another run, you can sometimes get better results. The docking protocols may also use random numbers, so doing several runs with the exact same starting positions and conformations can give a range of results. Is it possible to use the output from one run as the input for a second run? Perhaps the second run will do better. 

Have you read the documentation for ligand_docking at http://rosie.rosettacommons.org/ligand_docking and  http://rosie.rosettacommons.org/ligand_docking/documentation ? Have you read the articles listed on each of these pages? You can often get better answers by sending e-mails to the authors listed in these articles or on these web pages. You should refer these authors to your post here so they can post answers here that will help other users who have similar questions.

Another suggestion is to look for similar questions in the other Rosetta Forums. Also, if you examine the output files from the ligand_docking protocol, you might find Rosetta code. Perhaps you can use keywords from this Rosetta code to find Rosetta documentation that will help you.

I hope this helps. Good luck!

AdoCbl

The ligand conformers input is not necessarily in the location where the ligand is — Rosetta will translate/rotate the conformers onto the ligand in its docked position when it does the conformer sampling. Also, it’s a known issue that PyMol smashes all the confomer output together into a single structure. Rosetta still should be able to recognize that they’re separate conformers.

Instead of the LG_conformers.pdb file, you should ideally be looking at  the protein_LG_????.pdb files from the results table. These should show your ligand in the docked final location. (It should be a slightly different location for each result, but all in the same general area.)

Could you link to an example of one of your docking runs? If I can get a look at what your input and results look like, I might be able to say something further on what’s going on.