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Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

Post Situation: 

Centroid mode minimization

Category: 
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

Post Situation: 

Rosetta Antibody: Unable to open file and terminates

Category: 
Compilation

Hello, please note I'm revising my posting with some major updates, apologies to the 9 viewers who have come here prior as this will read completely different.

 

I'm encountering a read error with antibody_H3. Below is the executable I ran (I've also reproduced the error with .static mode):

mpiexec -np 4 $ROSETTA3/bin/antibody_H3.cxx11threadmpiserialization.linuxgccrelease \
  @abH3.flags

abH3.flags looks just like:

Post Situation: 

PyRosetta on Ubuntu 16.04 build error

Category: 
Compilation

- OS type/version/arch:
Linux Ubuntu 16.04  (on an Azure virtual machine)
- Python version:
3.5

- Version of PyRosetta including SVN revision number.
PyRosetta4.Release.python35.ubuntu.release-236.tar.bz2

- Version of Rosetta:
Rosetta 3.11 for Linux

 

Hello, I've installed PyRosetta and upon importing in Python3.5 I receive the following error:

Post Situation: 

Confusion for Input Tutorial

Category: 
Compilation

Hi All,

I have downloaded Rosetta 3.11 and built it with Scons.py using 

$ ./scons.py -j 4 mode=release bin 

The building of the binaries seems to work correctly providing me with:

scons: done building targets.

 

I am now attempting to familiarize myself with Rosetta by traversing the tutorials starting with the Input & Output Tutorial so I am within this directory:

Post Situation: 

compiling with intel c++ compiler

Category: 
Compilation

Intel compiler has problem dealing with defaulted and virtualized copy assignment operator, reported here.

https://software.intel.com/en-us/forums/intel-c-compiler/topic/837004

Because of this bug, compilation with intel compiler fails at `rosetta_bin_linux_2019.35.60890_bundle/main/source/src/protocols/genetic_algorithm/Entity.hh` line 55.

By implementing it explicitly, or removing "virtual" seems to be a solution.

 

Post Situation: 

running in MPI mode and multiple scores per output PDB file?

Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

Post Situation: 

GrowLigand

Category: 
Small Molecules

Hi all,

Anyone with experience with the GrowLigand mover?

I have as input a holo.pdb structure with a protein target of interest and a small molecule inhibitor which binds with low affinitty (parametrized to be used with genpot). 

I was hopping that this mover would return possible modifications on the ligand so I could rationalize my next steps of synthesis.

Here is my RosettaScripts:

Post Situation: 

cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?

Category: 
Design

Hello Forum

I'm trying to run fixbb on my cluster here, and everything seems to have been going well for a while, but it suddenly stopped and spit out the following in the log file:

Post Situation: 

Speed problem when running RosettaLigand ligand docking

Category: 
Docking

Hello, I am trying to do protein design using a protocol derived from RosettaLigand ligand docking.

When I run Rosetta Design as the following command line, everything seems correct and there are output structures (pdb files). The problem is that it takes ages to get the results. In average, it will take 15~20 mins to get one models. For 1000 models, it spent 9 days. I think there is something wrong, but I don't know how to solve it.

Post Situation: 

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