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Confusion for Input Tutorial

Submitted by mcguirst on Wed, 2019-11-20 12:29
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:

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Rosetta 3 - Build/Install

compiling with intel c++ compiler

Submitted by m-yoshimura on Tue, 2019-11-19 21:06
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.

 

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Rosetta 3 - Build/Install

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

Submitted by dantimatter on Wed, 2019-10-30 09:42
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!  

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Rosetta 3 - Applications

GrowLigand

Submitted by allan.ferrari on Sat, 2019-10-19 05:32
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:

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Rosetta 3 - Applications

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

Submitted by dantimatter on Wed, 2019-10-16 14:59
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:

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Rosetta 3 - Applications

Speed problem when running RosettaLigand ligand docking

Submitted by Nicole Deng on Tue, 2019-10-08 04:29
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.

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Rosetta 3 - Applications

Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database

Submitted by Corvin on Tue, 2019-10-01 02:04
Category: 
Fragment Generation

Dear fellows,

my recent situation with setting up the fragment generation for structure prediction ab initio consists in follow:

- It seems as if I solved my problems with version compatibility of gcc-compiler and the environment variable FRAGMENT_PICKER.

- But a problem with installation of updated make_fragments.pl and install_dependencies.pl is still remained unsolved. I carried out next actions with the ncbi-blast-2.9.0+-src package:

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Rosetta 3 - Applications

Ligand question - aromatic bonds not being enforced?

Submitted by Rick_Baker on Wed, 2019-09-11 09:08
Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

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Rosetta 3 - General

Options "-out:prefix" didn't work

Submitted by maruhuang on Tue, 2019-09-10 05:42
Category: 
Structure prediction

Hello everyone.

I used AbinitioRelax application to predict structure and added "-out:prefix ab"  into options.

The log shows " protocols.abinitio.AbrelaxApplication: Finished ab_0001 in 169 seconds." but I still got "S_00000001.pdb" file. So I can't simulation on multiple CPUs.

Any help would be appreciate.

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Rosetta 3 - Applications

"Make_fragments.pl" can't connect to dependencies links

Submitted by Corvin on Wed, 2019-09-04 23:54
Category: 
Structure prediction

Dear fellows,

I am studying to generate fragments for structure prediction ab initio locally, on my laptop (OS - Linux OpenSUSE), with a help of appropriate script "make_fragments.pl". I met with several problems during its running.

Firstly, "make_fragments.pl" can not connect to dependencies links. When I run such command, as "~/rosetta_bin_linux_2019.22.60749_bundle/tools/fragment_tools/make_fragments.pl name.fasta >& make_fragments.local", it gives me such error:

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