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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: 

antibody protocol fails

Category: 
Structure prediction

Hello,

I'm using antibody protocl to graft some models but it fails with the following error:

File: src/protocols/antibody/grafting/chothia_numberer.cc:152
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!

Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.

Thanks a lot in advance,

Best

Post Situation: 

Ab initio structure prediction for long amino acid sequence

Category: 
Structure prediction

Hi

I'm a postgraduate student, interested in protein structure prediction.

I noticed that the document said:

  • Abinitio: max 150 amino acids are cosidered possible

So, I want to know, how to use rosetta to predict number of protein of  amino acids more than 150 (e.g. 500)?

Post Situation: 

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