Raise better error in top-parser

[BartBruininks]

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]

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

[BartBruininks]

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

[fgrunewald]

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