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
| Attachment | Size |
|---|---|
 refine-xml.txt | 4.46 KB |
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
~