Small Molecules

Hi all,

I created a customized ligand, and we want to sample different rotamers around certein bonds by changing the torsion angles. And below is what we have done and we ran into an issue:

atom1 = AtomID(13,1)

atom2 = AtomID(14,1)

atom3 = AtomID(15,1)

atom4 = AtomID(16,1)

old_torsion_angle = pyrosetta.rosetta.core.conformation.Conformation().torsion_angle(atom1, atom2, atom3, atom4)

print (old_torsion_angle)

Hello all,

I wanted to conform Rosetta params for Methane molecule which I have written (as molfile_to_params.py fails to create). Also, is there any specific method to create params compounds with no rotamer?

Hi everyone, 

I am trying to read a pdb file that  has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads:

Hello！

These are many .wts file in database\scoring\weights.
I  don't clearly know which weight is used in which occasions,
and  just use score function according to papers.

I  read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
 and its recommend references.