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Can you provide a dummy example to get atomic partial charges please for an AM1 simple case ?
this line Hf, Etot, Eelec, Enuc, Eiso, EnucAB, e, P, charge, notconverged in test1.py return charge b…
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Hi there,
we want to compute partial charges for proteins in PDB format. We use the [Gasteiger](http://www.rdkit.org/Python_Docs/rdkit.Chem.rdPartialCharges-module.html#ComputeGasteigerCharges) alg…
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Hi, I want to build a protein-ligand system where the ligand has more than 150 atoms.
Here is my script:
```
def read protein(protein_file):
protein = pdbfile.PDBFile(protein_file)
retu…
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**Describe the bug**
https://github.com/openforcefield/openff-toolkit/blob/fd5a20b6094ac0f64f66510f2791244e9e5ef9b4/openff/toolkit/utils/openeye_wrapper.py#L224
This method detects the presence of…
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### Model Name
DelFTa quantum mechanical properties prediction
### Model Description
DelFTa predicts quantum-mechanical properties of drug-like molecules. It uses 3D message-passing neural networks…
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I'm getting this error when assigning partial charges using openeye's am1bccelf1 via the openff-toolkit:
```
def gen_charges(smc):
offmol = smc.to_openff()
offmol.assign_partial_charges(…
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**Describe the bug**
When loading a malformed mol2 file where all bond orders are 1 and partial charges are present, the implied formal charge is different from the partial_charges.sum(), and `create…
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## Environment Information
Open Babel 3.1.0
Linux, Ubuntu 20.04.4 LTS
## Expected Behavior
I wanted to perform forcefield calculations using partial charges from a file.
## Actual Behavior
…
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Although we typically serialize `GufeTokenizable`s to `dict`, `keyed_dict`, or `KeyedChain` forms turned to JSON, it can also be convenient to pickle these objects in certain cases. When using `multip…
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In the course of debugging #2, I noticed that the partial charges on `CTerminal/PRO/PRO.mol2` are kinda weird [1]. This may be related to an error message that pops up during system generation [2].
…