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RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()

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RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()
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Dear Rosetta Users, 

I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:

[FILE]: src/core/conformation/util.cc

[LINE]: 654

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::check_good_cutpoint_neighbour(): The selected residue is neither an alpha-, beta-, or gamma-amino acid, nor a peptoid, nor a sugar, nor a nucleic acid, nor an oligourea.  Nevertheless, it has a cutpoint variant type.  This should not be possible.

[END_MESSAGE]

[END_CRASH_REPORT]

 

or

 

[FILE]: src/core/conformation/util.cc

[LINE]: 678

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::check_good_cutpoint_neighbour(): The connected residue is neither a peptoid, nor an oligourea, nor an alpha-, beta-, or gamma-amino acid.

[END_MESSAGE]

[END_CRASH_REPORT]

 

There are no non-standard residues and/or co-factors, sugars, nucleic acid, etc… in the input files. The same inputs run on the ROSIE server without any problem.

In certain cases Rosetta generates more than 19500 structures and then crashes, in other cases the crash occurs earlier.

 

I’m running Rosetta 3.12 with MPI (rosetta_src_2020.08.61146_bundle). 
The width of my low-resolution scoring grid is 30 Å and the box size is 10 Å, since the length of the ligand is about 15 Å.
I’m performing 1000 cycles of low-resolution MC sampling, 12 cycles of high-res docking and repacking every 3th cycles.

 

It’s worth noting that I’m getting a lot of the following error too:

core.optimization.LineMinimizer: (9) [ ERROR ] Inaccurate G! step= 9.53674e-07 Deriv= -3.65573 Finite Diff= 0.663073

but reading other posts it doesn’t seem to be a problem.

 

Please find attached the options file that I’m using and the ROSETTA_CRASH.log.

 

Thank you in advance for your kind help!

Samuele

AttachmentSize
options.txt473 bytes
ROSETTA_CRASH.log8.12 KB
Category: 
Post Situation: 
Thu, 2021-03-25 09:32
sam_dc

I'm wondering if the issue is related to your inclusion of the -pH_mode related flags. There could be an issue with the interaction of the ligand docking code with the pH mode code. (That is, for some reason the pH-specific residue types could be seen as "not protein" by the ligand docking code.)

Note that Rosetta, by default, operates at physiological pH. You don't need extra flags to tell Rosetta to operate at standard physiological conditions. The -pH_mode and related flags are more for specialist protocols which are explicitly considering the pH dependence of things. They haven't really been tested extensively with the other operating modes of Rosetta.

Thu, 2021-04-01 08:56
rmoretti

Dear rmoretti,
I can confirm that the problem was caused by the -pH_mode related flags.

Thanks for your help solving this problem.

Mon, 2021-04-12 07:22
sam_dc