As you said for croos docking experiment.. I have started doing that but I am having some problems as its new for me..
1) As per the tutorial , I have created a parameter file for my phosphate ion using molfile_to_paramfile.
2) Next, I prepared the receptor for docking by suing the lingand_rpkmin command . Here after generating the 10 structures how can I select the best one for further docking ..
3) Okay say I ahev selected one structure , the next step is to provide the native structure.. I have it for my protein but phosphate ion is present in the crystal structure. So in this case shall I provide the native structure without phosphate ion one or not ??..
4) Finally, coming to actual docking how to give the number of steps the dockign should continue … and how large should this number be in mycase ?
After running the docking command I am getting the following errors :-
ERROR: Pose has no jumps!
ERROR:: Exit from: src/protocols/ligand_docking/LigandBaseProtocol.cc line: 272
Here is the list of parameters that I used :-
-start_from 0.000 0.000 0.000 (as I want rosetta to search for binding site, like in case of blind docking)
-mute core.util.prof ## dont show timing info
Pls help …