# Docking

## Extracting a part of a silent file as another silent file

Category:
Docking

Dear all,

I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.

First, I extracted the top 10% by sorting the I_sc with:

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## Flex-pep-docking (ab-initio mode)

Category:
Docking

Hello all,

To perform the Flex-pep-docking protocol (ab-initio mode), I need to create fragment files for the target peptide (with 8 residues). I have tried to do this with the make-fragment.pl script . However, I get the attached error. I have already installed the last version of Blast tools. please let me know what is the problem and how it can be solved?

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## covalent ligand docking in Rosetta

Category:
Docking

Hello,

I am modeling an enzyme and a substrate to study the enzyme specificity. From literature, I learned that the specificity is determined by the second step of the mechanism in which the ligand is covalently bound to D281 of an enzyme (see the attached picture showing the mechanism). Is Rosetta able to do covalent ligand docking? If so, how can I parameterize the ligand (which is covalently bound to the protein)? If not,  can I do covalent docking with other software(??) and then score it with Rosetta?

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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.

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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

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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