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Hi all,

I'm trying to use simple_cycpep_predict with crosslinker BBMB, and the generated structure (see attached) does crosslink with BBMB.  However, it also does a head-to-tail cyclization between the 2 termini and I would like to not have that happen.  It's not clear to me from the help file how to do that as the default uses head-to-tail cyclization.  Is there a way to turn that off?

Here is the sequence file, the parameters that I'm using, as well as one of the generated structures to illustrate what I am having issues with.

Hello world, 

How can I dock one protein into interface between two proteins? I am new to rosetta software and I am still leraning. I study a protein that bridges two other proteins togeter and I was wondering how can I model that? I would apreciate your input in directing me to the tutorials or documentation. 

Thanks. Cheems

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