After going through the tutorials of protein protein docking, I totally got in a mess.
The flag file and XML file, low resolution and hign resolution docking, clustering seem to mix together.
1. $docking_protocol.linuxgccrelease -database $ROSETTA_DATABASE @flag > log.txt
The flag file as follows:
-dock_pert 8 5
The low_res_docking.xml contents as follows:
2.It seems that the low resolution docking process encompasses high resolution docking as in the XML file.
So then I don't know how to make a high resolution flag file and XML file.Could you please list a general pipeline of protein protein docking? And is there any reference flag and XML file?
I am also not sure about the important parameters that I should set according to my protein. The manual seems not so much comprehensive...