Hello, i am trying to relax an enzyme with a co-factor (nadp) but whenever I do, the resulting structure looks wrong.
I use the NADP structure from pubchem as a starting point, then molfile2params structure and copy paste the returned LG_0001.pdb to my protein.
i then run the following code:
init("-default_max_cycles 200 -ignore_unrecognized_res 1 -ex1 -ex2aro -ignore_zero_occupancy false -fa_max_dis 9") #read paramsfile and pdb file and create initial pose ligand_params = [LG1.params] pose = pyrosetta.rosetta.core.pose.Pose() if len(ligand_params) != 0 and ligand_params != "": ligand_params = pyrosetta.Vector1(ligand_params) res_set = pose.conformation().modifiable_residue_type_set_for_conf() res_set.read_files_for_base_residue_types(ligand_params) pose.conformation().reset_residue_type_set_for_conf(res_set) pyrosetta.io.pose_from_file(pose, "pathtopose.pdb") scorefxn = create_score_function("ref2015_cart") pose_relax = pose.clone() scorefxn = create_score_function("ref2015_cart") relax = pyrosetta.rosetta.protocols.relax.FastRelax() relax.set_scorefxn(scorefxn) relax.cartesian(True) relax.apply(pose_relax)
however when i run this and dump the resulting pdb file, what i end up with looks like this:
https://imgur.com/a/riWsjOL (sry having issues displaying the image)
Does anyone know what causes this?
thanks in advance,