Stepwise Monte Carlo – errors with ResidueTypeSet and Disulfides

[Anonymous]

I am trying to run the Stepwise Monte Carlo protocol, and I can successfully run the demo (Rosetta/3.8/demos/public/stepwise_monte_carlo_protein_loop/) as written in the demo with #cycles=2, however if I try to increase the -cycles parameter so that the design can actually be fully completed (i.e. -cycles=50), the run stops with an error about variant residues (see error 1 below), which are not present in the sequence specified in the input fasta, and that are not inteded to be sampled. This error pops up with different ‘variant residues that can’t be found’ over different runs.

When I try to run the procedure on my own input files, I run into a different error where it seems Rosetta is getting thrown off by disulfides in the structure (see error 2 below).

Any ideas as to what’s going on? Appreciate any help!

P.S. I have attached input fasta and pdb files. Other input files from the demo are here: 3.8/Rosetta/demos/public/stepwise_monte_carlo_protein_loop/rosetta_inputs/

 

#commands

stepwise.static.linuxgccrelease -s noloop_mini_1alc_H.pdb -fasta mini_1alc.fasta -native mini_1alc.pdb -score:weights stepwise/protein/protein_res_level_energy.wts -silent swm_rebuild.out -from_scratch_frequency 0.0 -allow_split_off false -cycles 30 -nstruct 1

stepwise.static.linuxgccrelease -s P3_stepwise_13p.pdb -fasta P3_stepwise_13p.fasta -score:weights protein_res_level_energy.wts -from_scratch_frequency 0.0 -allow_split_off false -monte_carlo:submotif_frequency 0.0 -cycles 100 -nstruct 1 

 

#error 1 (variant residues)

protocols.stepwise.monte_carlo.StepWiseMonteCarlo: Embarking on cycle 23 of 30

protocols.stepwise.monte_carlo.StepWiseMonteCarlo: Modeling: 1-13 20-28

protocols.stepwise.monte_carlo.mover.ResampleMover: About to remodel move_element Choice RESAMPLE_INTERNAL_LOCAL res 12 with attachments  BOND_TO_PREVIOUS:11 BOND_TO_NEXT:13

protocols.stepwise.monte_carlo.mover.ResampleMover: Going to set up TRANSIENT_CUTPOINT_HANDLER with remodel_suite 11 cutpoint_suite 12

ERROR: unable to find desired variant residue: GLY:C_methylamidated GLY CUTPOINT_UPPER

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 671

[0x15a2c5b]

[0x6f67970]

[0x698c7de]

[0x5212a59]

[0x52134da]

[0x155953b]

[0x1708146]

[0x152bef1]

[0x152ddc8]

[0x152e4c9]

[0x14d6ec4]

[0x14d82be]

[0x14cf4d0]

[0xaad83a]

[0xaae873]

[0x40a6a6]

[0x7415626]

[0x741581a]

[0xaabf79]

caught exception

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueTypeSet.cc line: 671

ERROR: unable to find desired variant residue: GLY:C_methylamidated GLY CUTPOINT_UPPER

 

#error 2 (disulfide)

protocols.stepwise.monte_carlo.StepWiseMonteCarlo: Embarking on cycle 39 of 50000

protocols.stepwise.monte_carlo.StepWiseMonteCarlo: Modeling: 21-26 [ other_pose: 1-13 27-265]

protocols.stepwise.monte_carlo.mover.AddOrDeleteMover: Choice ADD res 26 with attachments  BOND_TO_NEXT:27

protocols.stepwise.modeler.align.StepWisePoseAligner: RMSD 0.000 (0 atoms in 21-26), superimposed on 758 atoms in 1-13 27-265 (RMSD 0.0000025)

protocols.sampler.protein.util: Using ProteinMainChainStepWiseSampler. Num poses: 135

ERROR: Could not find disulfide partner for residue 7

ERROR:: Exit from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 623

[0x15a2c5b]

[0x6f67970]

[0x514be14]

[0x5153bf8]

[0x5146780]

[0x54cdf90]

[0x54d58ff]

[0x1763dbc]

[0x17c16f5]

[0x176c05d]

[0x1615a4a]

[0x1601711]

[0x1603b7a]

[0x16f8025]

[0x16f9f5e]

[0x152bf22]

[0x152ddc8]

[0x152e4c9]

[0x14d6ec4]

[0x14d82be]

[0x14cf4d0]

[0xaad83a]

[0xaae873]

[0x40a6a6]

[0x7415626]

[0x741581a]

[0xaabf79]

caught exception

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 623

[Anonymous]

Protein stepwise hasn’t been very well supported in ~8 years, to be honest, since it hasn’t been an active area of development. The variant issue is something I’ve seen before, and you likely need to impose some additional flags to turn off certain “modern” moves to get the demo to run longer. I will try to share those flags soon.

As to your own file, I don’t actually see it as an attachment – only the demo file.

[Author]

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