search

graeter-group / colbuilder

Building collagen fibrils from amino acids sequences
Apache License 2.0
0 stars 0 forks source link

build_sequence error #10

Closed ncyx closed 2 weeks ago

ncyx commented 2 months ago

Encountered error:

Error in build_sequence: local variable 'formatted_output_pdb' referenced before assignment

Traceback (most recent call last):
  File "../main_sequence.py", line 414, in build_sequence
    formatted_output = work_dir / formatted_output_pdb.name
UnboundLocalError: local variable 'formatted_output_pdb' referenced before assignment

Config: 

mode: null
config_file: test_tar-1726655567.yaml
debug: false
sequence_generator: true
fasta_file: homosapiens.fasta
output_prefix: my_collagen_sequence
species: Homo_sapiens
crosslink: false
n_term_type: null
c_term_type: null
n_term_combination: null
c_term_combination: null
geometry_generator: false
file: null
output: collagen_output
working_directory: ./
contact_distance: 60.0
fibril_length: 334.0
crystalcontacts_file: null
connect_file: null
crystalcontacts_optimize: false
mix_bool: false
ratio_mix: null
files_mix: null
replace_bool: false
ratio_replace: null
replace_file: null
topology_generator: false
force_field: amber99
johibuck commented 1 month ago

I think the problem is that there are no crosslinks- the error message is missleading but if I change the crosslink settings to "true" the error disappears... :D @debora-monego maybe knows better why no crosslinks are not working yet.