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Docking

partial charge of params file in ligand docking

Category: 
Docking

Hello,

I am performing Rosetta ligand docking and I generated the .params file for the ligand with molfile_to_params.py file. I was wondering whether the partial charges in the .params file generated in this way are reliable. Or do I need to do DFT calculation or use another method to get the correct partial charges? 

Any suggestion is appreciated.

P.S: I obtained the ligand pdb file from rcsb and then convert it to sdf file. Then I generated the conformers with BCL and finally use molfile_to_params.py.

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Rosetta Ligand Ensemble

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/)

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Meaning of Metalbinding_constraint

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).

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residue_energy_breakdown of a protein-ligand complex.

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 :

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Issues with modifying dock.xml for multiple ligand docking

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. 

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multi ligand docking using rosetta script

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

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Ligand being read as part of protein structure

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

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