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Fragment Generation

fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so

Category: 
Fragment Generation

I'm sorry... I'm sure this is just something basic I overlooked but I'm not sure how this is happening since it seems that a basic component is missing....

I have Rosetta compiled with "extras = mpi" and I have OpenMPI installed.

I ran:

(mpirun --mca btl_tcp_if_exclude lo,virbr0 --hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err

Post Situation: 

Error_fragment_generation

Category: 
Fragment Generation

Hi

I was running makefragments.pl for my short length peptide (sequence length 6), as a pre-requirement for abinito FlexPepDock, and I am getting the error:

Error: expected creation of t001_.200.9mers after running  "/path/to/make_fragments.pl/fragment_picker.static.linuxgccrelease @t001__picker_cmd_size9.txt -j 1'!

It was working fine before, but with two abnormalities:

a. It was generating only 3 and 9 mers(no 5 mer): so I corrected the make_fragments.pl, where in "my @fragsizes" definition "5" was missing.

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fragment_picker.boost_thread.linuxgccrelease needed!!!

Category: 
Fragment Generation

Hello!

does anybody know where i can find this: fragment_picker.boost_thread.linuxgccrelease ?

I downloaded rosetta_2014.35.57232_bundle.tgz but the folder rosetta_2014.35.57232_bundle/main/source/bin is empty.

Thanks in advance

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how to generate Fragments using up to 2001 structures only

Category: 
Fragment Generation

Hello!

I am trying to replicate an old experiment and I'd need to generate fragments using old structures only. How can I do that?
at the moment I created a database of old structures and I downloaded the rosetta fragment picker tool so I am trying to find out what internal database of rosetta I should update, any suggestions?

Thanks a lot in advance

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Access to latest CS-ROSETTA tools

Category: 
Compilation
Structure prediction
Fragment Generation

Have been trying to access the latest CS-ROSETTA tools without success for several days. Looks like www.csrosetta.org has been down for a while.

Any alternative to www.csrosetta.org to access latest cs-rosetta tools?

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Robetta fragments and silent.out-file

Category: 
Fragment Generation

Hello,
I have a question about the robetta fragment-file. what does the numbers mean?!

1ofd A 1068 S L -163.692 159.068 168.636 -0.177 4.773 84.262 3 0.000 P 1 F 1
1ofd A 1069 P L -59.041 138.502 179.354 -0.177 4.773 84.262 3 0.000 P 1 F 1
1ofd A 1070 L L -65.398 -35.892 176.967 -0.177 4.773 84.262 3 0.000 P 1 F 1
Are the first free values angles?!

I have the same understanding problems with the silent.out file.

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Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

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ConstantLengthFragSet(3)..read_fragment_file RuntimeError

Category: 
Fragment Generation

Hello ~
I'm interested in Pyrosetta
and learning the tutorial
Workshop #4: PyRosetta Folding
page 4
11. Create a new subroutine in your folding code for an alternate random move based upon a “fragment insertion”. A fragment insertion is the replacement of the torsion angles for a set of consecutive residues with new torsion angles pulled at random from a fragment library file. Prior to calling the subroutine, load the set of fragments from the fragment file:
fragset = ConstantLengthFragSet(3)

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Error when running FRAGMENT generation

Category: 
Fragment Generation

Dear all,

I try to follow protocol and want to have fragment picker components for running Flexpepdock ab-initio protocol. But program return the ERROR. Can someone give me solution.

Thank alot for that.

this is my flag:
-s SPI.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-vall vall.dat.apr24.combo.v2.mar10.bfactor.v2

-frags:bounded_protocol

-frags:n_frags 200
-frags:n_candidates 200

-frags:frag_sizes 3
-frags:scoring:config quota_scores.wghts

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