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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.
When going through the rosetta tutorials, I see that the vall database is old, and I want to build new vall database.
could you please let me know how to efficiently build new vall database from PDB structures. When I run pdb2vall, it gives me this:
Usage: pdb2vall.py [options]
I am performing abinitio structure prediciton of a 382 long protein sequence by following the tutorial:
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:
-Precision-7920-Tower:make_fragments.pl -verbose myfasta.fasta no id specified. parsing filename instead. cannot parse id from filename so using 't001_' ID: t001 CHAIN: _ File for psipred not found! Generating from scratch instead. picking fragments with options: DEBUG: 1 add_pdbs_to_vall: chain: _ cleanup: 1 csbuild_profile: 0 exclude_homologs_by_pdb_date: 0 f: myfasta.fasta fastafile: t001_.fasta
I nearly ran out of space after running "install_dependencies.pl". Among the programs it installs, /database folder whcih includes "nr" sizes up to 657 GB. Can you please let me know if this is possible?
When I try to model a protein from the PDB (4WYH) I follow the abintio protocol correctly and generate fragments from Robetta. Yet I do not get a funnel shaped plot after 25,000 decoys.
Though it’s sequence clearly folds into this particular structure (as proved by the crystal structure) why can’t abinitio performs a successful simulation and result in a funnel shaped plot?
I am trying to run "make" in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7", follwing the installation instructions in "pdb2vall.README"; however, when running "make", I get this error (error is very long, so I have pasted the first and last lines of STDOUT) :
I am trying to perform ab initio structure prediction by following the tutorial: