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No disagreement on the current priorities described in #1 , but of the many options available to include in version 2, I would be interested to see additions to dataset towards larger solvated peptide…
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I tried the following script to get Hoomd forcefields from a topology and this error is raised when the `base_unit` argument is not passed to the function.
**Script:**
```python
import foyer
im…
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Hello!
I recently started using openmmforcefields package and absolutely love it! Thank you very much to all the developers!
I like the idea of parameterizing molecules on the fly, but I also wo…
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**Describe the behavior you would like added to mBuild**
The way that mBuild currently functions appears to be that bond, angle, and dihedral types are ordered according to the order that the molecul…
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At one point, we had separate FF files floating around for water (TIP3P) and ions. Currently, this does not seem to be the case (at least not in this repo) which means that someone applying our FF to …
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I am trying to use openff's parameters in my simulations using OpenMM. However, I am getting error that my ligand parameters (coming from openff-toolkit) have a different lj14scale scaling than openMM…
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Relevant reading: https://github.com/openforcefield/openforcefield/issues/5
We're working on versioning all unversioned `smirnoff99Frosst` files from the repo. This requires putting a version on lo…
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Debian Bullseye/Jupyterlab
Copied making-it-rain-main files and sub-directories to Miniconda/envs/Jupyterlab/CC. Opened CHARMM_GUI in Notebook. Here are the results:
Open In Colab
Hello the…
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**Bug summary**
I am trying to type a molecule using proper dihedrals but am receiving an error saying that the dihedrals can't be found:
Exception Traceback (m…
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**Describe the bug**
`Molecule.to_rdkit()` can produce a `Molecule` with a different number of atoms than the source RDKit molecule.
This appears to be because the `hydrogens_are_explicit` flag is…