So, I am trying to set up my docking experiment between two proteins.
I had read that for blind docking one should use the flag: -fake_native.
When I do this, I get the error: "Option matching -fake_native not found in command line top-level context"
Does this mean that "-fake_native" is no longer a flag option? And if so, is there a flag to replace it?
I no longer have a copy of 3.2.1 to check against, but an easy test is "docking.(Whatever) -help | grep fake_native". If zero show up, it's gone. If two or more show up, then you need to namespace it properly, so it will be something like (these are guesses) -docking:fake_native to discriminate it from -somethingelse:fake_natve. It's definitely gone from 3.3 and developer trunk.
I think fake_native was only used for RMSD calculations anyway and can be dropped with no consequence.
I just typed -help without "grep" and I couldn't find the listing for the flag -fake_native. So, it must not be in 3.2.1.
Thanks for the info, will proceed without it.