Comments (2)
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
from auto_martini.
The --fpred
argument worked fine.
Thanks,
Sam
from auto_martini.
Related Issues (20)
- "Missing parentheses in call to 'print'." HOT 15
- Max. number of attempts: 54517 HOT 1
- VisibleDeprecationWarning
- Improving molecule sanitization HOT 1
- auto_martini as an interoperable component HOT 2
- auto_martini fails 4 tests
- auto_martini doesn't work for silica coarse graining HOT 1
- setup.py
- The CG model for ethanol is different from the original paper HOT 1
- martini3 HOT 3
- ALOGPS can't predict fragment HOT 2
- Installation instructions are incomplete HOT 5
- No Metadata for AutoMartini HOT 5
- Meets ValueError when testing example molecules HOT 6
- ValueError: setting an array element with a sequence HOT 4
- pytest fail HOT 5
- Can we ask one bead per heavy atom? [question] HOT 2
- How many heavy atoms can be processed[no reply required]
- Installation not working HOT 7
- Problems with installation
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