openff-toolkit

openff-toolkit copied to clipboard

Example for putting a ligand into a box of water and equilibrating it

9

@slochower shared the following script with me, which seems to touch on some very useful areas. We should polish in into a full-fledged example! Some complications toward making this into...

j-wags

Bad optimized geometry for sulfonic and phosphonic acids

10

A Drugbank molecule with sulfonic and phosphonic acids optimizes with smirnoff99Frosst to bad geometries: valence angles O-P,S-O too large or small, S-O-H angle too small, and 1-4 distance O=S-O-H too...

cbayly13

Proton transfer in antechamber AM1 partial charge calculation

19

**Describe the bug** _originally posted by Bill Swope_ > Alberto and I have been looking at dipole moments for our neutral benchmark molecules and have discovered several issues that we...

j-wags

Raise exception when processing molecule with radical electrons

2

Here's a block to add to the changelog, keeping it out of the tree to make merges easier: ``` - [PR #1236](https://github.com/openforcefield/openff-toolkit/pull/1236) raises [`RadicalsNotSupportedError`](openff.toolkit.utils.exceptions.RadicalsNotSupportedError) when [`Molecule.from_openeye`](openff.toolkit.topology.Molecule.from_openeye), [`Molecule.from_rdkit`](openff.toolkit.topology.Molecule.from_rdkit), [`Molecule.from_smiles`](openff.toolkit.topology.Molecule.from_smiles), or similar...

mattwthompson

Canonical order before conformer generation

6

Fixes #926 - [x] Tag issue being addressed - [ ] Add [tests](https://github.com/openforcefield/openff-toolkit/tree/master/openff/toolkit/tests) - [ ] Update docstrings/[documentation](https://github.com/openforcefield/openff-toolkit/tree/master/docs), if applicable - [ ] [Lint](https://open-forcefield-toolkit.readthedocs.io/en/latest/developing.html#style-guide) codebase - [ ] Update [changelog](https://github.com/openforcefield/openff-toolkit/blob/master/docs/releasehistory.rst)

ijpulidos

Make utility function to save PDB file from Topology

5

I was running a super short minimization/simulation and wanted to output a PDB of the OpenFF Topology to check that it had worked properly. However, we have a way to...

davidlmobley

`OpenEyeToolkitWrapper.to_file` writes PDB files with no CONECT records

2

**Describe the bug** A `Molecule` written to a PDB file **includes** CONECT records when OpenEye Toolkits are **not** available but **excludes** them when they **are**. This can lead to surprising...

mattwthompson

PDBs written using OpenEyeToolkitWrapper don't contain atom names from OFFMol

2

**Describe the bug** ``` from openforcefield.topology import Molecule from openforcefield.utils.toolkits import RDKitToolkitWrapper, OpenEyeToolkitWrapper mol = Molecule.from_smiles('CCO') mol.generate_unique_atom_names() mol.to_file('test_oetkw.pdb', file_format='pdb', toolkit_registry=OpenEyeToolkitWrapper()) ``` yields a pdb file without unique atom names ```...

j-wags

Spec for undefined stereochemistry

16

## Purpose Because it's a complicated topic, and to maintain the ability to restart this discussion in the future, I think it's important to record our design decisions with regard...

j-wags

thiophene gets only 1 C atom type, but 2 different C-C bond lengths

9

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...

micaela-matta