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Membrane Abinitio modeling error

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Membrane Abinitio modeling error
#1

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

Post Situation: 
Thu, 2020-10-29 03:30
jkyan007

Sorry I can't help with your question, but how did you get the run_lips.pl script to work properly? Everytime I try it it crashes due to an uninitialized value and I end up with a bunch of empty files.

Tue, 2020-11-17 10:35
noahC_noahDo