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Recommendations for CoupledMoves enzyme redesign

Category: 
Enzyme Design

I'm preparing to start an enzyme redesign project using Rosetta, but the paper I'm supposed to be working off used the older enzdes application, which doesn't seem to be compatible with newer scorefunctions and sampling methods. CoupledMoves seems preferable, and I was hoping to get some recommendations for putting together a ligand docking and design protocol. I have basic familiarity with Rosetta, but since I'm the only person in my lab using it right now, I'd really appreciate any advice to help speed up the process and reduce time spent on trial and error.

Post Situation: 

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: 

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