You are here

Home

Docking

Rosetta Ligand Ensemble

Submitted by malfonsoprieto on Wed, 2021-05-26 10:21
Category: 
Docking

Dear Rosetta community, 

In our group we are interested in using the RosettaLigandEnsemble (RLE) protocol  (https://doi.org/10.1021/acsomega.7b02059). 

Since we are new to Rosetta, we decided to start by executing the RLE protocol with the example input files provided with the Rosetta source code

(i.e. /PATH/TO/ROSETTA/main/demos/protocol_capture/rosettaligand_ensemble/)

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Meaning of Metalbinding_constraint

Submitted by Corvin on Wed, 2021-05-19 07:54
Category: 
Docking
Scoring

Dear Sir and Madam,

Would anyone here be kind to explain the following statement about metalbinding_constraint or send the relevant paper?:

1. The (bio)physical meaning of metalbinding_constraint. I would like to find out, the underlied forces and energies, including such thermodynamical parametres, as enthropy, enthalpy and so on and so forth. Hereby, the next question arises from this point.

2. How this 'metalbinding_constraint' is calculated (I mean the formula, but, nevertheless, I am open to any explanation).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

residue_energy_breakdown of a protein-ligand complex.

Submitted by sam_dc on Tue, 2021-05-18 04:45
Category: 
Docking

Dear Rosetta Users, 

I'm using the "residue_energy_breakdown" utility in order to obtain a per-residue energy breakdown of the residues that interact with the ligand in my protein-ligand complex generated by the RosettaLigand application.

In the POSE_ENERGIES_TABLE at the end of the docked model I read quite reasonable energy terms :

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Issues with modifying dock.xml for multiple ligand docking

Submitted by DGR95 on Fri, 2021-05-14 12:51
Category: 
Docking

Hello all, 

I've been having some issues in modifying my dock.xml file for a multiple ligand docking run. I been trying to use the paper "RosettaLigand docking with flexible XML protocols" as a reference but no luck. According to the paper I should be trying to modify the <LIGAND_AREA> and <INTERFACE_BUILDER> taggs, but the paper only shows an xml file for a single ligand dock. I'm pretty new to this and rosetta scripts, so I'm not sure exactly how to proceed. Anyhelp would be appreciated. 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

multi ligand docking using rosetta script

Submitted by syntekabio2019 on Tue, 2021-04-13 19:31
Category: 
Docking

 

  Hi all.

  I'm trying to dock  my ligand with HEM to CYP using rosetta script with XML protocol

  overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and  ligand as separate entity

  But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.

  For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Ligand being read as part of protein structure

Submitted by MarkusAurelius on Thu, 2021-04-01 11:00
Category: 
Docking

Hi,

I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error: 

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

 chain_id W does not exist

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Protein Ensemble RosettaLigand Docking

Submitted by sam_dc on Fri, 2021-03-26 10:18
Category: 
Docking

Dear Rosetta Users, 

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

 

Thanks in advance.
 

Samuele

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Pages

Subscribe to RSS - Docking