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Problems with waters in CoupledMoves application

Submitted by Corvin on Tue, 2021-11-16 07:16
Category: 
Structure prediction
Docking
Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

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Rosetta 3 - Applications

small molecule charge generated by molfile_to_params.py

Submitted by rohi on Wed, 2021-03-17 09:35
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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Rosetta 3 - General

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

Submitted by Corvin on Wed, 2020-12-16 04:58
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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Rosetta 3 - Applications

where is generate_ligens.linuxgccrelease?

Submitted by Nicole Deng on Thu, 2020-12-03 00:00
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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Rosetta 3 - Applications

Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Submitted by Corvin on Wed, 2020-12-02 04:00
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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Rosetta 3 - Applications

Prevention of the negatively charged Nitrogen protonation by coupled_moves

Submitted by Corvin on Wed, 2020-11-18 02:56
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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Rosetta 3 - Applications

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

Submitted by Martin Floor on Thu, 2020-09-17 06:01
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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Rosetta 3 - Applications

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