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C-term amidation

Category: 
Design

Hello,

I have been trying to use the Cterm_amidation patch, but everytime I use it in FastDesign or scoring it turns it back into a regular C terminus.

I've read the posts from other users, but I still can't make it work... What am I doing wrong?

Things I've tried so far:

I added "-include_patches Cterm_amidation" flag, both with the input file having a regular C terminus and with a neutral terminus - in this case I made sure the names of the atoms matched these in the patch:

Post Situation: 

Error from clean_pdb.py

Category: 
Structure prediction

Dear Rosetta Users,

I'm recently studying the Comparative Modeling tutorial: https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

When I ran the script: clean_pdb.py, there was an error: /dors/meilerlab/apps/Linux2/x86_64/bin/python2.5: bad interpreter: No such file or directory.

What can I do to fix this? The python on my computer is python 3. Thank you in advance!

Post Situation: 

error in installing rosetta for use in phenix

Category: 
Compilation

Hi everybody!

I'm trying to install Rosetta (version 3.10) for use in Phenix on Ubuntu 20. No problem with Phenix installation, but when I run "rosetta.build_phenix_interface nproc=2" I got the following:

Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix
False
/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source

Post Situation: 

error in installing rosetta for use in phenix

Category: 
Compilation

Hi everybody!

I'm trying to install Rosetta (version 3.10) for use in Phenix on Ubuntu 20. No problem with Phenix installation, but when I run "rosetta.build_phenix_interface nproc=2" I got the following:

Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix
False
/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source

Post Situation: 

antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages

Category: 
Loop Modeling

Hello all,

I am trying to model the H3 loop of a nanobody (VHH). The protocol runs fine and completes successfully but it gives a lot of the following error messages:

......

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -0.121688 Finite Diff= 0.149698

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -0.0181975 Finite Diff= 0.0799868

Post Situation: 

Running RosettaScripts, but got an error "src/utility/options/OptionCollection.cc, line 1153, No values of the appropriate type"

Category: 
Design

Hello,

I'm a new user wants to run a RosettaScripts with disulfize mover, but right after I start the scripts, I got the following crash report. Any comments or suggestions on how to solve the issues? Thanks a million.

Post Situation: 

An error occurred during the installation

Category: 
Compilation

Dear Rosetta Users,

I recentlly downloaded the src version of rosetta 2020.50 and compiled it with scons.py, but there was an error. It seems that the program was pointing towards a wrong directory (the bin version directory) for the generate_database_cache application. I'm attaching the log file. Thank you in advance!

Post Situation: 

Remodel and the depracated EMPTY NC

Category: 
Design

I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.

I am using Remodel in Pyrosetta 4 2020.49 release (a stable)  for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.

Post Situation: 

ERROR: Not complementary at positions

Category: 
Structure prediction

Hi Rosetta team,

    I am trying to generate some tertiary structures for a relatively large RNA (300+ nt) with rna_denovo. But I keep getting a strange error saying the nucleotides are not complementary:

[ ERROR ]: Caught exception:


File: src/core/pose/rna/RNA_SecStruct.cc:286
[ ERROR ] UtilityExitException
ERROR: Not complementary at positions C   48 and G   53
 

    I attached my secondary structure, fasta and ct file for the RNA. I wonder what's the cause of this problem. Thanks much.

Post Situation: 

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