I am quite new to Rosetta. I have a very simple questions regarding general concepts about ligand-docking. I am a little bit confused about how to set parameter to ensure that all conformers generated can be tested. Lets say if I have a PDB containing 50 conformers. If I set -nstruct = 1 and run docking.xml with transformer like this (Transform name="predock" chain="X" box_size="20" move_distance="2" angle="20" cycles=“500” repeats=“2” temperature=“5”/>). What does really happen through the docking simulation?
Sub-question 1: Random conformer conf.A will be picked at the initial defined position -> run Monte Carlo cycle to minimize the score defined in “Transform”. The question is will other conformers be tested if -nstruct is set at 1? Since I got single PDB file and I really don’t know whether other conformers been tested or just randomly tested conf.A only.
Sub-question 2: Repeats defines as “Number of times to perform cycles from starting position”, will it use different conformer or just use the same one?
Sub-question 3: if I have two transform as follows.And I define the protocol to run transform 1 first and followed by transform 2. So, when we run protocol, does all cycles have been finished in transform 1 and the best pose will be transferred to transform 2? or, every accepted pose will go through transform 2? And generally, my question is the protocol will finished by stepwise, which means, mover one is finished totally then mover 2 start, or it works in continuous cycle format, in which cycle 1 in mover 1 finished then mover 2 started … so on so forth.
Add mover = Transform 1: 500 cycle (it is not correct script, just for illustration)
Add mover = Transform 2: 500 cycle
Add mover = final minimization (I guess this is for output file, choose the best pose for the whole protocol to report, since I only get one PDB output if -nstruct = 1)