You are here

Home

Unsolved

The problem hasn't been solved

cryptic error message from remodel in rosetta_scripts

Submitted by petrikigor on Mon, 2012-12-03 15:13

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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Rosetta repacking output

Submitted by doranhen on Mon, 2012-12-03 03:44

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?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

"Local sequence-structure compatability" in "design of ideal protein structures"

Submitted by petrikigor on Sun, 2012-12-02 09:25

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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

pNNMAKE compilation

Submitted by adva on Sun, 2012-12-02 03:59

Hello,
I'm trying to make fragments using rosetta 3.2 in order to run membrane ab initio protocol.
after trying to create pNNMAKE.gnu using "make" command I got this error:

----------------------------------------------------------------------
SYSTEM SETUP [make.system]
COMPILER=gnu @ adva
F77=g77
FFLAGS=-finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit -O -ffast-math -malign-double
FOPTIMFLAGS=-O -ffast-math -malign-double
FDEBUGFLAGS=-g -Wall -Wimplicit -Wsurprising -Wformat -W
FPROFILEFLAGS=-pg
LINKFLAGS=

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

fa_plane enregy term in scoring weights

Submitted by ytao on Fri, 2012-11-30 20:25

Hi,

I'm working on a protein that appears to have some aromatic groups stacking in the x-ray structure, but I could not see such conformers in my models(Ca RMSD 1.1 A to X-ray structure) built with rosetta.
I found there is this term "fa_plane" in the scoring weights that is supposed to describe "pi-pi interaction between aromatic groups, by default = 0", however, there's no scoring method defined for it in the source code. So if I change the weight of this term, it will only give an error message: "ERROR: Requested ScoreType fa_plane does not have a registered EnergyMethodCreator."

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

How to use -cst_fa_file and -relax:constrain_relax_to_native_coords at the same time

Submitted by Anatol on Thu, 2012-11-29 14:12

Hi:

I would like to relax my X1.pdb structure with the atom coordinate constraints relative to the backbone atoms of another structure X2.pdb and some other constraints given in -cst_fa_file constrains.
Here is what I have done:

relax.linuxgccrelease -database /home2/ruvinsky/simcode/rosetta_database -in:file:s X1.pdb -in:file:fullatom -out:file:fullatom -relax:fast -score:weights score12_full -out:pdb -ex1aro -ex1 -ex2 -out:nstruct 10 -relax:constrain_relax_to_native_coords -in:file:native X2.pdb -cst_fa_file constraints

It failed with the following error message:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

too many constraints result in no output pose

Submitted by Yao Wu on Sun, 2012-11-18 23:45

Hi,everyone.
When I applied 11 distance constraints, get from chemical cross-linking assay, into Protein-Protein docking, there is no output pose and also no error reported.
Here is the output log:
"""
protocols.jd2.JobDistributor: poseinp_0001 reported failure and will retry
... ...
protocols.jd2.JobDistributor: poseinp_0012 reported failure and will retry
"""

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Missing movers in OSX PyRosetta

Submitted by lah435 on Fri, 2012-11-16 15:45

The RigidBodyMovers are missing in the OSX build of PyRosetta. Examples: On Ubuntu: In [3]: help(RigidBody RigidBodyDofPerturbMover       RigidBodyMover RigidBodyDofRandomizeMover     RigidBodyPerturbMover RigidBodyDofRandomTransMover   RigidBodyPerturbMover RigidBodyDofSeqPerturbMover    RigidBodyRandomizeMover RigidBodyDofSeqRandomizeMover  RigidBodySpinMover RigidBodyDofSeqTransMover      RigidBodyTransMover RigidBodyDofTransMover

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Pages