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Raise better error in top-parser #338

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BartBruininks opened this issue Aug 11, 2023 · 3 comments
Open

Raise better error in top-parser #338

BartBruininks opened this issue Aug 11, 2023 · 3 comments
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enhancement New feature or request

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@BartBruininks
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BartBruininks commented Aug 11, 2023

Describe the bug
Turorial brush lipids does not finish. Polyply 1.5.0.

polyply gen_coords -p system.top -o struct.gro -res PEO OHter -c bilayer_brush.gro -name test -box 8.0 8.0 33.0 -split POPE:HEAD-NH3:TAIL-PO4,GL1,GL2,C1A,D2A,C3A,C4A,C1B,C2B,C3B,C4B -b build_file.bld

yields the following output with an error:

polyply gen_coords -p system.top -o struct.gro -res PEO OHter -c bilayer.gro -name test -box 8.0 8.0 33.0 -split POPE:HEAD-NH3:TAIL-PO4,GL1,GL2,C1A,D2A,C3A,C4A,C1B,C2B,C3B,C4B -b build_file.bld
INFO - step - reading topology
INFO - step - processing topology
Traceback (most recent call last):
  File "/home/bart/.virtualenvs/containment/bin/polyply", line 258, in <module>
    main()
  File "/home/bart/.virtualenvs/containment/bin/polyply", line 254, in main
    subprogram(**args_dict)
  File "/home/bart/.virtualenvs/containment/lib/python3.8/site-packages/polyply/src/gen_coords.py", line 198, in gen_coords
    topology.preprocess()
  File "/home/bart/.virtualenvs/containment/lib/python3.8/site-packages/polyply/src/topology.py", line 238, in preprocess
    self.gen_pairs()
  File "/home/bart/.virtualenvs/containment/lib/python3.8/site-packages/polyply/src/topology.py", line 270, in gen_pairs
    comb_rule = comb_funcs[self.defaults["comb-rule"]]

Expected behavior
The creation of the brush bilayer. I altered the name to just bilayer.gro as I did the mushroom and brush tutorial in separate folders.

Additional Files
brush.zip

@fgrunewald
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@BartBruininks your topology file is incorrect. You forgot to include #include "martini-3/martini_v3.0.0.itp"

@BartBruininks
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You are completely right. Thanks for the quick response. All is working now.

@fgrunewald
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Let's keep this open, the top parser should raise a more legible error

@fgrunewald fgrunewald changed the title comb-rule error in PEG lipid tutorial Raise better error in top-parser Aug 11, 2023
@fgrunewald fgrunewald added the enhancement New feature or request label Aug 11, 2023
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