Rosetta_scripts error, Got some signal… It is:6

[Anonymous]

Hi there,

I was trying to run this command:

#!/bin/bash



$ROSETTA3/bin/rosetta_scripts.linuxgccdebug 

-database $ROSETTA3_DB 

-in:file:fasta ./input_files/3j5pD.fasta 

-parser:protocol ./input_files/RosettaCM101.xml 

-nstruct 200 

-relax:minimize_bond_angles 

-relax:min_type lbfgs_armijo_nonmonotone 

-relax:jump_move true 

-relax:default_repeats 3 

-relax:dualspace 

-edensity::mapfile ./input_files/emcd101_TRPVI_chainD.mrc 

-edensity::mapreso 3.3 

-edensity::cryoem_scatterers 

-out:file:silent outCM$1.silent 

-out:path:all ./output_files/CM 

-out:suffix _101_$1 

-default_max_cycles 200 

But I get the following error,

rosetta_scripts.linuxgccdebug: src/core/pose/Pose.cc:965: void core::pose::Pose::set_phi(utility::pointer::ReferenceCount::Size, core::Real): Assertion `( residue_type(seqpos).is_protein() || residue_type(seqpos).is_peptoid() || residue_type(seqpos).is_carbohydrate() ) || print_backtrace( "residue_type(seqpos).is_protein() || residue_type(seqpos).is_peptoid() || residue_type(seqpos).is_carbohydrate()" )' failed.

Got some signal... It is:6

Process was aborted!

 

The command has worked for me in the past using a different sample. I have also tried it without the -relax:minimize_bond_angles option but with the same results.

Thank you for the help,

-Joshua

[Anonymous]

It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.

Do you have any non-protein residues in your input structure? (or in any of your templates?)

[Anonymous]

It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.

Do you have any non-protein residues in your input structure? (or in any of your templates?)

[Anonymous]

It’s kinda hard to say exactly what’s wrong without seeing the full backtrace, but it looks like it’s an issue with your input structure.

Do you have any non-protein residues in your input structure? (or in any of your templates?)

[Author]

Posts