RosettaAntibody3 core.pose.util error

[Anonymous]

I’m using rosetta_src_2020.08.61146_bundle. I’m trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the following command:

module load rosetta/2020.08 blast/2.10.0+ gcc/9.1.0

antibody.default.linuxgccrelease -ignore_unrecognized_res true -fasta IL6antibody.fasta -out:path:all antibodied

Here is the IL6antibody.fasta file:

>heavy

EVQLVESGGKLLKPGGSLKLSCAASGFTFSSFAMSWFRQSPEKRLEWVAEISSGGSYTYYPDTVTGRFTISRDNAKNTLYLEMSSLRSEDTAMYYCARGLWGYYALDYWGQGTSVTVSS

>light

QIVLIQSPAIMSASPGEKVTMTCSASSSVSYMYWYQQKPGSSPRLLIYDTSNLASGVPVRFSGSGSGTSYSLTISRMEAEDAATYYCQQWSGYPYTFGGGTKLEIK

This is the error (with part of the preceding logging messages):

protocols.antibody.grafting: Sequence after:  EVQLVESGGKLLKPGGSLKLSCAASGFTFSSFAMSWFRQSPEKRLEWVAEISSGGSYTYYPDTVTGRFTISRDNAKNTLYLEMSSLRSEDTAMYYCARGLWGYDYWGQGTSVTVS

core.conformation.Conformation: Found disulfide between residues 22 96

core.conformation.Conformation: current variant for 22 CYD

core.conformation.Conformation: current variant for 96 CYD

core.conformation.Conformation: current variant for 22 CYD

core.conformation.Conformation: current variant for 96 CYD

protocols.antibody.grafting: Adjusting frl template sequence [/gpfs/fs1/sfw2/rosetta/src/rosetta_src_2020.08.61146_bundle/main/database/additional_protocol_data/antibody//antibody_database/1ay1_trunc.pdb]...

protocols.antibody.grafting: By using numbering: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108

core.conformation.Conformation: Found disulfide between residues 23 87

core.conformation.Conformation: current variant for 23 CYD

core.conformation.Conformation: current variant for 87 CYD

core.conformation.Conformation: current variant for 23 CYD

core.conformation.Conformation: current variant for 87 CYD

protocols.antibody.grafting: Sequence before: DIQMTQSPAIMSASPGEKVTMTCSASSSVSYMYWYQQKPGSSPRLLIYDSTNLASGVPVRFSGSGSGTSYSLTISRMEAEDAATYYCQQWSTYPLTFGAGTKLELKRA

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard





AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.





/var/spool/slurm/job15053608/slurm_script: line 5: 18463 Segmentation fault      (core dumped) antibody.linuxgccrelease -ignore_unrecognized_res true -fasta IL6antibody.fasta -out:path:all antibodied

This occurs whether I use the antibody.linuxgccrelease or the antibody.default.linuxgccrelease executable, and whether I have the flag -ignore_unrecognized_res or not.

Thanks for your attention.

[Author]

Posts