Docking

Hi all,

          we are trying to run protien -ligand docking. We were able todo succesfully the tutorial and do for some of our drug molecules except "Diltiazem". we generated conformers using online tool [mentioned in the tutorial] and tried schrodinger conformers too. but the following error still persists. Screen shot is attached.

'Translate' mover" chain X doesnot exist.

We checked the conformers pdb file every conformer is seperated by 'TER' text and both PDB and conformers file has chain X.

Hello,

I ran protein-protein Rosetta docking for 50 output structures. The I_sc of the output structures (50 structures) are so close to each other in such a way that their standard deviation is so close to zero(around 0.03). I was wondering what this means. Does it make sense MC sampling of Rosetta gives me identical results?

Thank you

Hi, I am using mol-to-param script to generate param files of my conformer. the sdf file looks normal before generation. But the PDB looks weird with some bonds connected to each other when I visualize it in pymol software however it looks totally fine in chemdoodle3D. Anyone has any clue about this? 

The PDB with weird structure looks like this:

Hi,

We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.