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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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AssertionError: Hydrogens are not added. Please add Hydrogens #47

Open calvanid opened 4 years ago

calvanid commented 4 years ago

Hi, I used LigParGen locally and I have encounter an error like this with my system:

$ LigParGen -p opt.pdb -r UNL -c 0 -o 0 Warning!! 1.Cannonicalising Input MOL/PDB file 2.Atom ordering may change 3.But the Coordinates remain the same 1 molecule converted 31 audit log messages 1 molecule converted 31 audit log messages MOLECULE HAS A CHARGE of 0 Traceback (most recent call last): File "/vol/home/calvanid/anaconda2/bin/LigParGen", line 10, in sys.exit(main()) File "/vol/home/calvanid/anaconda2/lib/python2.7/site-packages/LigParGen/Converter.py", line 90, in main convert(**vars(args)) File "/vol/home/calvanid/anaconda2/lib/python2.7/site-packages/LigParGen/Converter.py", line 159, in convert ), "Hydrogens are not added. Please add Hydrogens" AssertionError: Hydrogens are not added. Please add Hydrogens

It's a molecule with only 30 atoms carbon atoms, but without hydrogens and fluorine atoms in their place.

Do you have any advice to solve this problem?

Thanks a lot for your time and waiting for your kind reply,

My Best Regards