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Small Molecules

Pyrosetta imported after rdkit

Category: 
Small Molecules

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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How to freeze ligand during FastRelax?

Category: 
Small Molecules

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.

 

Thank you

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GrowLigand

Category: 
Small Molecules

Hi all,

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:

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Modeling small molecules

Category: 
Small Molecules

Hi all,

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? 

 

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Ligand question - aromatic bonds not being enforced?

Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

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

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set_torsion_angle error

Category: 
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)

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Relax with multiple small molecules

Category: 
Small Molecules

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

-relax:respect_resfile
-packing:resfile resfile

it fails with the following message

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Reading chloride anions

Category: 
Small Molecules

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:

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