Docking

Hello,

So I am trying to run the D100_Docking.py on PyRosetta4 that I have installed on Windows 10 Bash shell. I am just trying to use the script as is before attempting my own PDB files. Below is what I did, along with the errors:

Any help is greatly appreciated!

(base) jrodriguez@DESKTOP:/mnt/c/Windows/system32$ cd /mnt/c/Users/jrodriguez/Documents/PyRosetta4

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?

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/)

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 :