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Hello Rosetta people,

I performed a protein protein docking of a protain A + ligand A (74 atoms) noted as binary_complex to protein B, and got warning of missing atoms, still could get docked P-P poses, however, the ligand is not intact, some atoms missed in the output binary_complex. I also added the -ignore_unrecognized_res flag in the command.

Hi,

I am trying to reproduce the the results from this paper 'Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps', but when I try to run the script from the paper (de3mo) i'm getting the following error:

File: src/utility/options/OptionCollection.cc:1467
Option matching -in:file:override_database_params not found in command line top-level context

Hi, I wonder if there is a general way to generate the correct params file of new beta and gamma NCAA  ? I am trying to parameterize a customized gamma amino acid residue for GenKIC application. I used the molfile_to_params_polymer.py to generate .params file from the .mol file attached below:

4CG.pdb

 OpenBabel04262311383D

 29 28  0  0  1  0  0  0  0  0999 V2000

   -5.3100   -4.8280    2.6840 N   0  0  0  0  0  0  0  0  0  0  0  0

Dear all,

I am designing some peptides with the anchor_design approach. I am using the dG_separated values to compare them. For this, I included an InterfaceAnalyzer mover in my anchor_design xml script as follows: