I'm following the design_with_ncaa demo to use MakeRotLib to parameterize a covalently modified residue, and MakeRotLib keeps crashing on my molecule with the following uninformative (to me) error:
$ $ROSETTA3/bin/MakeRotLib.default.macosclangdebug -options_file ../
../makerotlib_options_150_150_2.in
core.init: Rosetta version ea84b24e5e76c18fa3b964241f37e1a82a1ae9a8 2016-02-05 19:04:15 -0600 from git@github.com:RosettaCommons/main.git
core.init: command: /Users/ipqb/software/rosetta_src_2016-02-07/main/source/bin/MakeRotLib.default.macosclangdebug -options_file ../../makerotlib_options_150_150_2.in
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=618961100 seed_offset=0 real_seed=618961100
core.init.random: RandomGenerator:init: Normal mode, seed=618961100 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /Users/ipqb/software/rosetta_src_2016-02-07/main/database
protocols.make_rot_lib.MakeRotLibMover: Creating score function...
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.make_rot_lib.MakeRotLibJobInputter: Instantiate MakeRotLibJobInputter
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 385 residue types
core.chemical.ResidueTypeSet: Total time to initialize 5.28987 seconds.
protocols.make_rot_lib.MakeRotLibJobInputter: MakeRotLibJobInputter::fill_jobs
protocols.make_rot_lib.MakeRotLibJobInputter: pushing the omg: 180 bb2: 150 bb3: 150 eps: 180 bin
protocols.make_rot_lib.MakeRotLibJobInputter: pushed all jobs
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.make_rot_lib.MakeRotLibJobInputter: MakeRotLibJobInputter::pose_from_job
protocols.make_rot_lib.MakeRotLibJobInputter: filling pose from Job PYC
protocols.make_rot_lib.MakeRotLibJobInputter: Making a PROTEIN rotamer library...
ERROR: Failed to apply a PatchOperation to PYC
ERROR:: Exit from: src/core/chemical/Patch.cc line: 333
0 libutility.dylib 0x0000000117dce8e5 print_backtrace() + 53
1 libutility.dylib 0x00000001180af8cc 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) + 956
2 libcore.2.dylib 0x0000000115cd0a4f core::chemical::PatchCase::apply(core::chemical::ResidueType const&, bool) const + 1951
3 libcore.2.dylib 0x0000000115cd6408 core::chemical::Patch::apply(core::chemical::ResidueType const&, bool) const + 808
4 libcore.2.dylib 0x0000000115ec619d core::chemical::ResidueTypeSet::generate_residue_type(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 8973
5 libcore.2.dylib 0x0000000115ec3da0 core::chemical::ResidueTypeSet::name_mapOP(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 112
6 libcore.2.dylib 0x0000000115ec3a66 core::chemical::ResidueTypeSet::name_map(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 54
7 libcore.2.dylib 0x0000000115ec429b core::chemical::ResidueTypeSet::generate_residue_type(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 1035
8 libcore.2.dylib 0x0000000115ec3da0 core::chemical::ResidueTypeSet::name_mapOP(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 112
9 libcore.2.dylib 0x0000000115ec3a66 core::chemical::ResidueTypeSet::name_map(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 54
10 libprotocols_f.4.dylib 0x0000000109a990c4 protocols::make_rot_lib::MakeRotLibJobInputter::pose_from_job(core::pose::Pose&, std::__1::shared_ptr<protocols::jd2::Job>) + 5060
11 libprotocols.1.dylib 0x000000010fb9cab1 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) + 3809
12 libprotocols.1.dylib 0x000000010fb9a175 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 677
13 libprotocols.1.dylib 0x000000010fb270f5 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 149
14 libprotocols.1.dylib 0x000000010fb9a966 protocols::jd2::JobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>, std::__1::shared_ptr<protocols::jd2::JobOutputter>) + 566
15 MakeRotLib.default.macosclangdebug 0x000000010268689f main + 527
16 libdyld.dylib 0x00007fff901765c9 start + 1
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'PYC_0001'
Error:
[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/Patch.cc line: 333
ERROR: Failed to apply a PatchOperation to PYC
Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: PYC_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds
caught exception 1 jobs failed; check output for error messages
Attached are the mol file for my molecule with an acetylated N-terminus and N-methylated C-terminus (which I passed to molfile_to_params_polymer.py). I'm assuming there's a problem with my input files, but I haven't been able to find it. If anyone could point me to the right direction, I'd be very grateful.
| Attachment | Size |
|---|---|
 params file for molecule | 6.95 KB |
| mol file for molecule | 6.52 KB |
| MakeRotLib options file | 923 bytes |
Category:
Post Situation:
I've sent this along to a few folks who look NCAAs regularly. First reply:
"The issue isn't immediately obvious, but I've eliminated the possibility that seemed most likely from the phrasing:
> Attached are the mol file for my molecule with an acetylated N-terminus and N-methylated C-terminus
As desired, the params don't have an already-capped structure. (That would certainly mess with some PatchOperations.)
It's really big, though. Maybe the presence of atoms with names like OC, CP1, CM1/2, etc. is messing with the ability to add those atoms, since that seems reminiscent of patch atom names."
A followup:
"(If this turns out to be the problem and he doesn't want to change atom names, he can also use the explicit tripeptide method (i.e. ACE and NME residues) by using the flag -use_terminal_residues.)"
Hi smlewis, thanks for forwarding these replies. This is curious; the atom names were generated by the script packaged with the mentioned demo. I suppose it doesn't expect so many atoms that it would ever reach OC and CM/CP. I'll try renaming those specific atoms and report back whether that works.
Changing the atom names didn't work, but the "-use_terminal_residues" flag worked perfectly. Thanks!