You are here

Solved

The problem has been solved

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: 

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

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:

Post Situation: 

Ligand question - aromatic bonds not being enforced?

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

Post Situation: 

Options "-out:prefix" didn't work

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.

Post Situation: 

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

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:

Post Situation: 

how to restore "rosetta_scripts.default.linuxgccrelease"

Category: 
Compilation

Hi,

I have rosetta installed but when using it I accidently deleted rosetta_scripts.default.linuxgccrelease. I am wondering how I can get it back. Can anyone help me, please?

Thank you very much.

Jinyan

 

Post Situation: 

Structure prediction using true distance and angle constraint

Category: 
Structure prediction

Hello,

I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?

Post Situation: 

Pages

Subscribe to RSS - Solved