error–rosetta fragment‐based refinement protocol for refinement against EM density

[Anonymous]

I am trying to fit my pdb structure into EM density and the following information happened:

tupdens=======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MinMover – cenmin=======================

core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (1458)

Etable: 142 52  1 8

 

ERROR: Fatal Error in VDW_Energy

ERROR:: Exit from: src/core/scoring/vdwaals/VDW_Energy.cc line: 188

0   libutility.dylib                    0x000000010f2dbbeb print_backtrace(char const*) + 59

1   libutility.dylib                    0x000000010f2dba17 utility::exit(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 887

2   libcore.3.dylib                     0x000000010d5445c9 core::scoring::vdwaals::VDW_Energy::residue_pair_energy(core::conformation::Residue const&, core::conformation::Residue const&, core::pose::Pose const&, core::scoring::ScoreFunction const&, core::scoring::EMapVector&) const + 1545

3   libcore.3.dylib                     0x000000010d6b214a core::scoring::ScoreFunction::eval_twobody_neighbor_energies(core::pose::Pose&) const + 1146

4   libcore.3.dylib                     0x000000010d6ae217 core::scoring::ScoreFunction::operator()(core::pose::Pose&) const + 1255

5   libprotocols.3.dylib                0x000000010b12bafb protocols::simple_moves::MinMover::apply(core::pose::Pose&) + 1051

6   libprotocols.1.dylib                0x000000010bd3fc6f protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&) + 1183

7   libprotocols.1.dylib                0x000000010bd3a87e protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1422

8   libprotocols.1.dylib                0x000000010bf97a9f protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 7023

9   libprotocols.1.dylib                0x000000010bf953ec protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 332

10  libprotocols.1.dylib                0x000000010bf72dc2 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66

11  rosetta_scripts.macosclangrelease   0x000000010772528c main + 508

12  libdyld.dylib                       0x00007fff92e135ad start + 1

13  ???                                 0x0000000000000002 0x0 + 2

protocols.rosetta_scripts.ParsedProtocol: Exception while processing procotol:

protocols.jd2.JobDistributor: 

 

[ERROR] Exception caught by JobDistributor for job A-metal_0001_0010

 

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/vdwaals/VDW_Energy.cc line: 188

ERROR: Fatal Error in VDW_Energy

 

Please see attached xml

[Anonymous]

my flags:

 

#

# In production runs consider using atleast 10000

# Using the -in:path flag makes the “input tag” just the filename

-database /Applications/rosetta_58704_2016/main/database/

-in:file:s A-metal.pdb

# Since the important output is the feature database,

# ignore the job distributor output.

#-edensity:mapfile pic-itc-iis.mrc

#-out:suffix pic

-ignore_unrecognized_res

-edensity:mapreso 3.9

#-edensity:grid_spacing 2.0

#-edensity:fastdens_wt 20.0

-edensity:cryoem_scatterers

-parser:script_vars denswt=25 rms=1.5 reso=3.9 map=pic-itc-iis.mrc testmap=pic-itc-iis.mrc

-crystal_refine

-nstruct 10

#-auto_setup_metals

#-out:file:fullatom

-default_max_cycles 200

-overwrite

-parser:protocol refine.xml

-run:use_time_as_seed

~

[Author]

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