Docking

Hi there!

I follow the ligand docking tutorial from here: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

When I get to point 6 and try to run docking protocol via ./rosetta_scripts.linuxgccrelease @options it says ERROR: Cannot open file "3PBL_ETQ.pdb"

How can I check the particular path to the file and correct, if needed?

Thanks in advance!

I was preparing the ligand params file for docking. When I used the following command to generate params files, I always get the "Too many arguments!" error. 

​~/rosetta*/main/source/scripts/python/public/molfile_to_params.py \ -n XX -p XXX --conformers-in-one-file XXX.sdf 

How to fix this problem? Thank you in advance.

Hello,

This is a continuation of an earlier thread, but I am still having trouble getting the surface_docking application to accept my inputs of a protein and ice surface. After correcting issues with hydrogen naming and now using the -ignore_waters false flag so that rosetta does not delete the ice surface, I am still getting the following error (this was all the error output):

Hey,

So I ran a docking simulation in which I docked a small molecule to a dimer metal containing protein. I generated 1000 structures output into a  silent file. I wanted the top 10 scoring structures just to see if the run worked and used "grep '^SCORE' IPDock/IPDock.out > IPDock/IPDockScores" to extract scores, the sort command to order them and created a file with the top ten structures.