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Small Molecules

small molecule charge generated by molfile_to_params.py

Category: 
Small Molecules

Hello,

I am performing Rosetta Ligand docking for a ligand, let 's say A . The ligand A is in contact with both water and water vapor. I have two main quesions and I would really appreciate your help in this regard:

1. Do I need to explicity consider water in my docking as a separate ligand with the ligand A? Or is the implicit solvation in scoring function sufficient?

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Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Sir and Madam,

I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.

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where is generate_ligens.linuxgccrelease?

Category: 
Small Molecules

Hello, everyone!

I am reading Mr. Baker's paper titled "Computational design of ligand-binding proteins with high affinity and selectivity". In the supplementary data, they used generate_ligens.linuxiccrelease to generate ligand conformers. But I can't find generate_ligens tool in my directory (~/rosetta/bin), also I didn't find any record about it in Rosetta tutorials. Anyone konws where to find it?

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Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Rosetta people,

I am trying to dock ligand, which possesses by sulfonamide NH group to the target protein with a help of coupled_moves application by the following command:

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Prevention of the negatively charged Nitrogen protonation by coupled_moves

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear sir and madam,

I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:

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When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error

Category: 
Small Molecules

Hi everyone, 

I detected an issue with the small molecule-docking application using rosetta scripts and the setup for doing large-sized libraries screening. In this set up you generally use a "screening_job_file" input that specifies which combination of ligand and protein structures will be used during the simulation. This file looks something like this:

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what factors determine the lowest (best) LigInterfaceEnergy score?

Category: 
Docking
Scoring
Small Molecules

Hi everyone.

We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.

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