Open SGenheden opened 8 years ago
Try running from the refactor branch
git checkout refactor
the executable is slightly different:
python auto_martini.py --smi "c1ccc(cc1)C#N" --mol bni
You'll notice that if fails:
WARNING:main:ALOGPS can't predict fragment: N#Cc1[c][c][c][c][c]1
looks like the prediction algorithm wasn't trained against cyanide. You can always fall back on the atom-based Wildman-Crippen prediction algorithm (--fpred
):
python auto_martini.py --smi "c1ccc(cc1)C#N" --mol bni --fpred --aa bni_aa.gro --cg bni_cg.gro
which works on my end. However, you might want to check that the bead type assigned to the cyanide group is correct (the Wildman-Crippen isn't as good a prediction algorithm as alogps).
Cheers, Tristan
The --fpred
argument worked fine.
Thanks,
Sam
Having trouble parameterising some molecules with a nitrile group. With a simple benzonitrile:
auto_martini --smi "c1ccc(cc1)C#N" --mol bni
I get the following error message