polyply_1.0
polyply_1.0 copied to clipboard
Raise better error in top-parser
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