Solved

Hello Rosetta users,

I have a few questions with respect to antibody modelling in Rosetta, specifically I am trying to replicate the worked example in the recently published Nature Protocols article “Modeling and docking of antibody structures with Rosetta” (doi:10.1038/nprot.2016.180).

I am having a problem at the first stage in the process – Antibody homology modelling. In the paper, they run the antibody binary with some flags to avoid ‘cheating’, since the crystal structure of the sequence already exists within the pdb:

Hi,

I'm trying to run antibody.linuxgccrelease -fasta antibody.fasta|tee grafting.log but got this error

terminate called after throwing an instance of 'std::out_of_range'

  what():  basic_string::substr: __pos (which is 3) > this->size() (which is 0)

I am running rosetta_bin_linux_2016.15.58628_bundle and I would like to run a prediciton with a set of constraints which are defined by a potential using the ETABLE function.

As it was not implemented in the FuncFactory.cc file, I have added: 

#include <core/scoring/func/EtableFunc.hh> in the //Package headers

and 

FuncFactory::add_type( "ETABLE", FuncOP( new EtableFunc( 0, 0, 0) ) );

After that, I have recompiled and it worked to identify the Etable Function. :)

Hi