I have encountered a curious issue. If I import rdkit before pyrosetta, the latter will not work properly. Rdkit after pyrosetta works fine —so I am basically reporting it here (right place?). Both use Boost wrapping C++ IIRC, so I'm guessing Rdkit changes some setting or imports some library. This code block misbehaves:
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I want to fix (freeze) ligand during fastrelax because the fastrelax changes ligand conformation weirdly .
This happens even with params file of the ligand.
Therefore, I tried ignore_unrecognized_res, but this option just not outputting the ligand in the result file.
Here I attach screenshots.
Anyone with experience with the GrowLigand mover?
I have as input a holo.pdb structure with a protein target of interest and a small molecule inhibitor which binds with low affinitty (parametrized to be used with genpot).
I was hopping that this mover would return possible modifications on the ligand so I could rationalize my next steps of synthesis.
Here is my RosettaScripts:
Just trying to model a small molecule and how it interacts w/ my bigger protein in pyrosetta.
I got this far:
pose2 = Pose()
nonstandard_residue_set = generate_nonstandard_residue_set(pose2, ["ARA2.params"])
pose = pose_from_pdb(nonstandard_residue_set, "combine.pdb")
But pose_from_pdb only takes only 1 argument, how do I get around this?
I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py
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)
Fast relax works fine with two ligands when the .params file are provided in the format.
-extra_res_fa LG1.params LG2.params
But when the same protocol is used with a few added flags such as
it fails with the following message
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: