selecting pivot_residue in Backrub for ensemble generation

Without specifying a resfile, the sidechains aren’t repacked, “NATRO”, whereas you’d probably want them to change in conformation (“NATAA”) if you want to assess your protein’s plasticity.

You might want to try pumping the kT up. The default is 0.6 kcal/mol (which what you’d get at 25°C in a real system). Say, 1 kcal/mol (37°C) or higher. It is a statistical potential value so the temperature is far from real, so you can go much higher. 

Backrub is not really an MD run, it is meant for protein design with flexible backbone and the end result will be a protein in an energy minima. A better alternative is the cartesianMD mover: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/CartesianMD

• It’s a scripts/pyrosetta only, but has decent documention.
• It does what you’d expect: it rattles your protein at a given kT energy making it drift like a normal MD simulation —except in implicit solvent.
• It is okay with ligands
• It is cartesian and not internal coordinate mode though

For pyrosetta here is an example:

pose = pyrosetta.Pose()

params_paths = pyrosetta.rosetta.utility.vector1_string()

params_paths.extend([params_filename])

pyrosetta.generate_nonstandard_residue_set(pose, params_paths)

pyrosetta.rosetta.core.import_pose.pose_from_file(pose, pdb_filename)

md = pyrosetta.rosetta.protocols.md.CartesianMD(pose, pyrosetta.create_score_function('ref2015_cart'))

md.set_ncyc_premin(0)

md.set_ncyc_postmin(0)

md.set_nstep(500)

md.set_temperature(310)

md.use_rattle(True)

md.set_store_trj(True)

md.apply(pose)

ps = md.dump_poses(pose)

pyrosetta.rosetta.core.scoring.CA_rmsd(ps[1], ps[3])

print({'poses': len(md.dump_poses(pose)),

'kinetic_energy': md.kinetic_energy(),

'potential_energy': md.potential_energy(),

'score': pyrosetta.create_score_function('ref2015_cart')(pose),

'dofs': md.n_dof(),

'RMSD': pyrosetta.rosetta.core.scoring.CA_rmsd(ps[1], ps[3])}

)

params_filename is just a string of a path of a params file  (topology file, “ligand.params”) required to load the pose, if you have multiple add multiple to that list if you have none skip the second, third and four lines, it is equivalent to “-extra_res_fa”. Likewise, the string pdb_filename is your filename for your pdb, equivalent to -s.

The code was meant as an example snippet and not meant to be complete. It lacks the import and init of pyrosetta

import pyrosetta

pyrosetta.init(extra_options='-no_optH false -mute all -ignore_unrecognized_res true -load_PDB_components false')

And after the run you may want to dump any pose to PDB

pose.dump_pdb('whatever.pdb')

Additionally you may want to change the setting say:

md.set_ncyc_premin(200)

md.set_ncyc_postmin(0)

md.set_nstep(50_000)

In this example, as each step is 2 fs, that would be 100 ps. The number of poses in the list ps is one every 100 I think, so you’d have 500 poses, but worth checking that detail with a short run.