I need to create peptides to use them as flexible ligands in docking (DockThor platform). I'm new at pyRosetta so I've only seen 1 tutorial until now. I'm using the following code
from pyrosetta import *
from pyrosetta.toolbox import *
peptide_sequence = 'insert peptide sequence'
pose = pose_from_sequence(peptide_sequence)
scorefxn = get_fa_scorefxn()
# define variavel score before relax
score_before_relax = scorefxn(pose)
# Relaxa a pose
relax = pyrosetta.rosetta.protocols.relax.FastRelax()
# Calcula e imprime o score após o relaxation
score_after_relax = scorefxn(pose)
print('Sscore pre relax:', score_before_relax)
print('Score pos relax:', score_after_relax)
I don't know why but I can't insert them in DockThor platform, it shows an error when I try. When I open the .pdb pose in a text editor, there's no CONECT section as other .pdb files from cristalized peptides, I think maybe that can be the reason.
Is there some protocol to create small peptides (9~13 residues) for use in docking?