Hi,
I am modeling a 178 residue membrane protein sequence using the abinitio protocol
To briefly describe what I have done:
1. generate structure fragments using Robetta server
2. generate a span file using OCTOPUS server and the script, octopus2span.pl
3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl
4. generate PDB using membrane_abinitio2.linuxgccrelease
I can run the BRD4.fasta in the tests successfully following above protocols.
but running my sample error in the last step.
ERROR: can’t find residue type at pos 179in sequence MSGGKYVDSEGHLYTVPIREQGNIYKPNNKAMADELSEKQVYDAHTKEIDLVNRDPKHLNDDVVKIDFEDVIAEPEGTHSFDGIWKASFTTFTVTKYWFYRLLSALFGIPMALIWGIYFAILSFLHIWAVVPCIKSFLIEIQCISRVYSIYVHTVCDPLFEAVGKIFSNVRINLQKEI
ERROR:: Exit from: src/core/pose/annotated_sequence.cc line: 156
terminate called after throwing an instance of ‘utility::EXCN_utility_exit’
this is my last setp options
/home/rosetta-3.5/rosetta_source/bin/membrane_abinitio2.linuxgccrelease -in:file:fasta CAV1.fasta -in:file:spanfile CAV1.span -in:file:lipofile CAV1.lips4 -in:file:frag3 aat000_03_05.200_v1_3 -in:file:frag9 aat000_09_05.200_v1_3 -in:path:database /home/rosetta-3.5/rosetta_database/ -abinitio:membrane -membrane:no_interpolate_Mpair -membrane:Menv_penalties -membrane:normal_cycles 40 -membrane:normal_mag 15 -membrane:center_mag 2 -score:find_neighbors_3dgrid -nstruct 10 -out:pdb
Thanks for your help in advance.
Best
yan
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