Docking

partial charge of params file in ligand docking

Submitted by rohi on Fri, 2021-05-28 08:43

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

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/)

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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).

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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 :

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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.

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