# Docking

## Python2 script in Rosetta3.13

Category:
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 "!="

Post Situation:

## How to set start coordinates for ligand when doing protein_ligand docking

Category:
Docking

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

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## How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion

Category:
Docking

Dear Sir/Madam, in my .xml script, I wish to use a if_X_scoreterm,  from InterfaceScoreCalculator mover, such as interface_delta_X as GenericMonteCarlo criterion but this term cannot recognized by Rosetta. There is no such kind of score_type. I wonder if there is way to do so?

Thanks

Best Regards

Rico

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## 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?

Post Situation: