Unsolved

Hi,

I tried to use RosettaDock with protein-nucleic acid chains. But I have a problem. Rosetta doesn't seem to recognise nucleic acids with the parameters I used. Here is the error message:


ERROR: unrecognized aa U
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 534


The version of RosettaDock I compiled (3.2.1) worked with the protein-protein complexes I tried.

I suppose there is a command to specify nucleic acids or a specific database to use. Can anybody please tell me how to use RosettaDock for protein-nucleic acid chains?

Is there an argument flag that will suppress Rosetta output? Even better, one that will suppress all but errors?

Thanks.

I'm using the standalong version of Rosetta Antibody. I can rebuild the antibodys which are already in PDB, however, for my own sequences, I can not build them for some reasons. I checked the results of the CDR Graft procedure. I found the "FR02.pdb" was distorted. Apparently, the some atoms of H-CDR3 residues were far away from the framework. Besides, I got a "VERY LOW CONFIDENCE PREDICTION" warning on the H3 loop.

Goodmorning,

I'm currently experiencing some troubles while using the RigidBodyMovers and I hope someone could explain me this strange problem. I perform a rigid body move and calculates its energy. But the result is different if I evaluate the energy after having stored the pose in a .pdb. Here is the code.


// Creating the poses and the scoring function
core::pose::PoseOP pose = new core::pose::Pose();
core::scoring::ScoreFunctionOP score_fxn = core::scoring::ScoreFunctionFactory::create_score_function("standard");