The problem hasn't been solved
Dear all,
My problems as follows:
1）I repacked protein side-chains by the application of "relax.linuxgccrelease -score:dun08 -database .../... -in:file:s .../.... -nstruct". Does the default action as above call FixbbSimAnnealer FixbbSimAnnealer：：run()？
Hello everybody
doing
score_fxn5=create_score_function( 'score5' )
score_fxn2=create_score_function( 'score2' )
and printing them I obtain the same output, I thought they were meant to be different.
print score_fxn?
ScoreFunction::show():
weights: (vdw 1) (cenpack 0.5) (pair 1) (env 1) (cbeta 0.25) (hs_pair 1) (ss_pair 1) (sheet 1)
energy_method_options: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT
EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12
EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid
Hi,
I am running Rosetta for predicting a structure of a protein (target) using a homologous protein (template). The template does not cover the whole target structure. The parts that are not covered contain cysteins. Is it possible to fix those residues in a disulfide bridge? When I use -in:fix_disulf option, I get an error message:
"core.conformation.Conformation: [ERROR] Residue 322 is out of range."
I think Rosetta is fixing residues in the template, but not in the target protein. Is it possible to fix disulfides in the target protein?
Hi,
If I have a protein of size nres. And I do small moves at say residue x (< nres). Is there a way to keep residues x+1..nres at the starting coordinates, but allow residues 1..x to move?
x+1..nres forms an interface with its dimer partner and hence I do not want to move those residues.
Thanks,
Aroop
Can anyone provide straightforward instructions on how to get RosettaHoles2 to run?
From digging around the forums here it seems that it was included in 3.2 but undocumented, dropped in 3.3, planned to be included in 3.4, but wasn't. From what I can tell some functionality is available in RosettaScripts, but it's undocumented and unclear if it's Holes or Holes2. Some unreleased files were emailed to one user who may have gotten it to work in 3.4. Instructions on how to use it with 3.2 may have been emailed by the author to one user.
Hi all,
I have a scenario where I have a peptide-protein complex. I would like to thread a series of sequences over the peptide, then minimize the peptide-protein complex. The idea being, I would like to tell which threaded-peptide-sequences would be the "best" binder predictors. Or at least be able to segregate between potential non-binding sequences and binding sequences.
I've been looking at the backrub protocol. Would this be an appropriate application? I don't see immediately how I can thread the sequences over the peptide with this application then.
Hi everyone,
I'm trying to generate ligand conformers for redesigning an enzyme. I had an input conformation, but when using it to generate conformers, it gave me this error:
Loading internal fraglib
81736 fragments loaded in 0.65 seconds
Title = untitled
Can't assign MMFF type to atom number 44 S
Warning: force field setup failed due to missing parameters for molecule untitled
Can you give me some hints on solving this problem?
Thanks.
As per the guide on Kinematic Loop Modeling http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/df/d..., I am trying to pass -loops:refine_repack_cycles as an option to loopmodel.linuxgccrelease.
However, I get the following error message: ERROR: Option matching -loops:refine_repack_cycles not found in command line top-level context
