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I generated a table of images & info of the premade NCAA params in the database

Category: 
Chemically Modified Residues

I don't have a problem*, I just wanted to link to a possibly useful resource. Namely, I was playing around with primeval genetic codes and I wanted to to know what the 3-letter code was for one amino acid. As a result I wrote a small script to make a table of images, filenames and three letter codes.

https://github.com/matteoferla/Display-of-preset-Rosetta-NCAAs

Post Situation: 

Error in src/protocols/membrane/util.cc line: 1224

Category: 
Docking

Hi, I am trying to prepare a MPDocking run (v 2019.35).

Both prepacking as well as actual docking crash with the same message:

ERROR: The SpanningTopology object in MembraneInfo is empty!
ERROR:: Exit from: src/protocols/membrane/util.cc line: 1224

However, the attached log file seems to indicate that the molecule was read correctly. Also the TMspans were build and their center calculated (end of logfile).

 

 

Post Situation: 

FARFAR2 error

Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

Post Situation: 

ERROR ON MAC ROSETTA

Category: 
Compilation

Good afternoon,

I downloaded the rosetta bundle with binaries for the Mac. When trying to compile the suite with ‘./scons.py mode=release bin’ I keep getting this error message.

src/protocols/antibody/database/CDRSetOptionsParser.cc:81:8: error: reference to 'core' is ambiguous

        for ( core::Size i = 1; i <= core::Size(CDRNameEnum_proto_total); ++i ) {

              ^

src/core/types.hh:32:11: note: candidate found by name lookup is 'core'

namespace core {

          ^

Post Situation: 

get an increased energy after energy minimization when using different score functions for repacking and energy minimization

Category: 
Design

Hi, 

I am a new user of rosetta. Now I meet some problem that I cannot solve. I am wondering whether you could please help me. I would much appreciated. 

Post Situation: 

ROSETTA design affinity optimization

Category: 
Design

Hello

I'm trying to to use rosetta design (http://rosettadesign.med.unc.edu) to increase binding affinity between 2 proteins in 1 pdb file. 

I want 2 residue ranges to be mutated in chain B but all other residues to remain the same. Therefore I have used this resfile:

NATRO

start
71 - 88 B ALLAAxc EX1
50 - 56 B ALLAAxc EX1
 

However, the server mutates residues in both chains. How do I force it to only mutate chain B?

Post Situation: 

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