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
Category:
Post Situation:
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?)