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I'm starting a thread to discuss how we should best deal with small molecules.
I'd love for YANK to make use of the nice OpenMM app tools `Modeller` and `ForceField` to set up protein systems, but th…
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I have some code that generates XYZ geometries, and I need these to be converted into ExtXYZ frames. I can write these geometries to temporary files and read them back in as frames from those files, b…
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### Week 1 - Get to know the community
- [x] Join the communication channels
- [x] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Install Docker…
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For example, this input: `CC(C)(C)*OO` generates this stack trace.
```python
KeyError Traceback (most recent call last)
~/apps/aiidalab-widgets-base/aiidalab_widg…
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Hi,
I'm having issues right before the ESP calculation when the _-poleditin.txt is used in poledit. Despite using "addhydrogentocharged=False", _-poleditin.txt contains 4 more atoms (I suppose H at…
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Hi! I cannot get result file when run the tutorial.ipynb with followed error. Can you help me, thank you!
Isomer generation for job1
Enumerating cis/tran isomers for unspecified double bonds...
Enu…
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Hi everyone,
Just recently installed KinBot, and am trying to run the gvl_reactions example. I used the following to install pybel:
`conda install -c openbabel openbabel`
and am getting the…
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Hi,
I was trying to install kinbot locally sourcing from github. Due to python binding requirment or pybel for openbabel, which both did not work in my system. Therefore I installed kinbot and open…
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This is mostly an idea for a GSOC project. There's a bunch of cool stuff in rdkit which isn't even close to being in MDA (and vice versa) so rather than reinvent wheels, it would be cool to do:
```p…
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Most of the time using the PyBel (Openbabel 3.1.0) api in enzy_htp to protonate ligand will give a file with **"HETATM"** lines. (e.g.: test/preparation/test_protonate.py::test_pybel_protonate_pdb_lig…