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Trouble installing Rosetta 3.9 on MacOS Catalina

Category: 
Compilation

Hello, I am having trouble installing Rosetta 3.9 on my dual core Intel mac running MacOS Catalina. I am following the instructions from this website: https://new.rosettacommons.org/docs/latest/build_documentation/Build-Documentation

However, I am getting errors. May someone help me troubleshoot through this process? I have attached a text file with the commands I used and the errors I am getting.

Thank you in advance.

Johnny

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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.

Post Situation: 

The /main/source/bin directory is not created

Category: 
Compilation

Hello,

I am trying to compile rosetta_src_2021.16.61629_bundle.tgz and for this I follow the following steps:

  • tar -xvzf rosetta_src_2021.16.61629_bundle.tgz
  • cd rosetta_src_2021.16.61629_bundle / main / source /
  • ./scons.py -j6 bin mode = release> salida.txt

 

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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/)

Post Situation: 

FastRelax Refinement severe clashes

Category: 
Structure prediction

Dear Rosetta community,

I am working with Rosetta version 2020.08.61146. have run into an issue of massive clashes when refining a part of a ribosome structure using FastRelax. I have previously used Fast Relax extensivly as a preliminary refinement step and its usually works wonders. This has been on individual chains and now I want to try to relax an entire subunit however Fast Relax seems to tear a few nucleotides apart. I attached images pre and post FastRelax as well as my RosettaScripts XML and shell output. 

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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 :

Post Situation: 

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. 

Post Situation: 

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