Error while running MakeRotLib

[Anonymous]

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.

[Anonymous]

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.”

[Anonymous]

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.)”

[Anonymous]

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.

[Anonymous]

Changing the atom names didn’t work, but the “-use_terminal_residues” flag worked perfectly. Thanks!

[Author]

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