Docking

Good morning,

    I am trying to use Rosetta (v3.13) for  drug screening analysis and I 
    found a specific script in the Rosetta3.13 package (also in other 
    versions) which has some python2 code that hampers its use in the 
    current python3.

    The script is: 
    rosetta_bin_linux_2021.16.61629_bundle/main/source/scripts/python/public/batch_molfile_to_params.py

    Python2 code:

    1) Lines 110, 114, 117: print without brackets

    2) Lines 40, 116: "is not" instead of "!="

Hi,

I am new to rosetta and I want to perform protein-lignad docking using rosetta3.13, I used my own PDB files and the option.txt, dock.xml under the folder rosetta/main/demos/tutorials/ligand_docking to perform docking. I found the ligand was still outside the protein after docking. Therefore, I tried to add the start coordinates for the ligand in the dock.xml but didn't find a right way. Could you help me with this?  I attached the PDB file I used for docking.

Thanks,

Huanhuan

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:

sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat

Dear Rosetta Users, 

I'm going to run a molecular docking simulation of a tripeptide - small protein (around 150 aminoacids) complex.
The tripeptide consists of all D-amino acids and has about 20 rotatable bonds. 

Which application -- between RosettaLigand and FlexPepDock -- is better to dock such a small and high-flexible peptide ?
Moreover, I'd like to know which is the most up-to-date protocol to incorporate non-canonical amino acids into Rosetta.

Thanks in advance!
Samuele