Docking

Hello,

I want to get a series of enzyme-substrate binding pose in one step of my research, but I met some questions:

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

Hi there,

I am trying to run Flexpepdock for several peptides which have Cterm_amide group. I checked the ATOM TYPES for NH2 which are also correct but while reading pdb it always gives warning:

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 "!="