Comments (5)
Reproduced with the newest version of openbabel, I'll file an issue there.
As always, thanks for your work!
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After protonated by openbabel, the C
turned to C+
, which might not be correct.
Before:
After:
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After some digging, I found that Dimorphite-DL may be a good alternative to openbabel , which provide a reasonable protonated result.
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It does seem that this issue is related to Open Babel, it would be worth reproducing it outside of ProtoCaller in the newest Open Babel version and if the problem still persists, you should probably submit an issue there.
In any case, I added some basic (experimental!) checks to spot unphysical charges and fix them, so your example should work now. I pushed the update to the development branch, so you can get the update when the conda package is built.
Edit: Dimorphite-DL seems interesting, I will consider adding it to ProtoCaller.
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Hi @msuruzhon , use latest version of openbabel from conda should fix this, see openbabel/openbabel#2353
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Related Issues (20)
- Abnormal memory usage in protocaller HOT 13
- Can I use ProtoCaller in protein-protein system? HOT 4
- The merge has opened/closed a ring HOT 12
- An input file contains a line longer than 4095 characters HOT 4
- LINCS warning and structure clash HOT 7
- Can I supply a ligand coordinate file as input? HOT 1
- H bond constraint HOT 1
- How to supply a custom pdb file (without pdb id) for protein? HOT 2
- Memory usage constantly growing with the number of perturbations. HOT 6
- How to restore ligand from parametrised file? HOT 2
- Select chain from polymer HOT 5
- Molecule ID not found HOT 1
- Error while calling command 'antechamber' HOT 1
- minimise not take effect when protonated was set to True HOT 2
- Invalid file format for file HOT 2
- tleap failed for protein HOT 2
- Not all chains are contained in the FASTA sequence
- Installing error
- running error
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