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I'm working on adding an example to set up and run the entire FreeSolv set (in [this branch](https://github.com/choderalab/yank-examples/tree/freesolv/examples/hydration/freesolv)), and noticed that t…
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Hi,
![trial](https://user-images.githubusercontent.com/45015867/129105734-ea3e73df-f6e7-484c-80b2-808f60cda402.png)
![trial1](https://user-images.githubusercontent.com/45015867/129105747-eefb83b6-…
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Dear Developers
I begun to use MDSuite, and analyzed the ion conductivity from the lammps trajectory like,
ion_ne = LiTFSI_H2O_experiment.run.NernstEinsteinIonicConductivity(species=['Li'],da…
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Hi folks,
I am working towards a python-based workflow for the parameterisation of a library of aromatic polymer fragments. In the past, I used exclusively ambertools/tleap but I would like to speed…
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Hello,
I used the following script to calculate localized orbitals of an ethane
molecule using the Foster-Boys localization method. When looking at the
orbitals, numbers 4 and 5 came out delocalize…
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DeepChem Version: 2.1.0
Platform: OS; python 3.5
I have trained a Grid-Random Forest regression model on the PDBBind core dataset that has been featurized with the grid featurizer (loaded disk dat…
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**Description:**
- DeepChem Version: 2.1.1
- Platform: Linux Mint
I tried the dc.molnet.load_pdbbind(), according to the tutorial.
Then, some error came out. (Unable to add hydrogens mat…
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The issue is potentially related to issue #266.
The current definition of `_atom_type.symbol` reads:
```
The identity of the atom specie(s) representing this atom type.
Normally this code is the…
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Structure with collection code 133424 from ICSD (Pr Sm Pb Si2 S8) is read incorrectly by `Structure.from_file()`. In particular there should be 18 Pb2+ sites, but there are 30 after the read. There is…
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Those of us in the MD community would very much like to be able to take output from QM packages and take it directly into MD engines and chemistry toolkits we use. However, these typically require wha…