The problem hasn't been solved
Dear Rosetta Community,
I am trying to test run RosettaDNA protocol. For some background of the test, please refer to my early post on the forum: http://www.rosettacommons.org/content/rosettadna-error
-in:file:l inputs
the inputs file contains:
00_wildtype_0016_0001.pdb
00_wildtype_0016_0002.pdb
...
00_wildtype_0016_0203.pdb
all the input files are in the current directory.
The error is:
protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0201.pdb nstruct index 1
Hi,
I have both backbone NOE and sidechain NOE data for a small protein. When I specify the backbone NOE data during Abinito simulation it works fine with scoring penalties displayed in atom_pair_constraints column. But when I modify the constraints file for sidechains and supply it Relax or Score with "-constraints" flag it doesn't seem to make any change in the energies, I seriously doubt that It takes those constraints into account during relax. So my questions are:
1. Can relax take sidechain restraints?
2. Is there any special flag to supply during relax?
Hi all.
I am trying to add nucleotides to the 3 and 5 prime end of a dna strand. I have used this code to grab a nucleotide residue, thanks to smlewis and sergey:
chm = rosetta.core.chemical.ChemicalManager.get_instance()
set = chm.residue_type_set('fa_standard').get()
ade = rosetta.core.conformation.ResidueFactory.create_residue(set.name_map("ADE"))
I used prepend_polymer_residue_before_seq_pos and append_polymer_residue_after_seq_pos to add the nucleotides to the pose.
Hello everybody,
I do fragment-based loopmodeling which is performing well. Now I want to add a distance constraint to have a disulfide bond between two cysteines but something is going wrong and I get no output. What am i doing wrong?
My input file is:
Hi,
I was wandering if anyone can tell me what is the best way to resolve van der waals clashes in a model of a transmembrane protein using rosetta?
Thank you,
Doran
Does anybody know what this means or how to extract more information to solve the problem?
protocols.forge.remodel.RemodelMover: BUILD CYCLE REMAINING 1
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1980 residue types
protocols.forge.components.VarLengthBuild: VLB count_cutpoints 1 interval.left 113 interval.right 122
protocols.forge.components.VarLengthBuild: picking 200 10-mers for position 113
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Got some signal... It is:6
Hi,
I've used rosetta3.1 for model repacking using energy minimization, my command line was:
score.linuxgccrelease -database /share/apps/rosetta/rosetta_database/ -s test.pdb -score_app:linmin -score:weights standard -score:patch no_solvation -in:file:repair_sidechains -out:output
After this procedure, I discovered that one Asp in my model (just one of the Aspartic acids in the model, the rest are fine as far as I've noticed) has a covalent bond between its backbone carbonyl and its side chain carbonyl, creating a ring. That is weird, can anyone explain to me why this happens?
I'm not sure if this the best place to ask, but I couldn't think of anywhere better:
I read and was really impressed by the conclusions of Koga, et al. "Principles for designing ideal protein structures". One thing that really intrigued me was the step in the process described as filtering for "local sequence structure comparability". Neither the article nor the example code seem to indicate how this filtering was done. The example RosettaScripts code simply indicates## The filter for local sequence structure compatibility was done without using RosettaScripts
