-
The API for fragmenting is a little awkward:
```python
f = fragmenter.fragment.WBOFragmenter(mol, functional_groups=None, verbose=False) # some of the options go here
f.fragment(threshold=0.01, kee…
-
Keeping track of my thoughts so we can come back to this:
### Current Implementation
Both `Topology` and `ForceField` have `aromaticity_model` attributes. These are set to `OEAroModel_MDL` by d…
-
(This is related to #726, but different enough to warrant a new issue.)
@rafwiewiora in our lab has been working on ways to deal with the Zn2+ ions [found in ~10% of all PDB structures](http://dx.doi…
-
Hope installed it.. But returns following WARNING...
$:amber.python -m pip install gmx_MMPBSA
Collecting gmx_MMPBSA
Downloading gmx_MMPBSA-1.0.0-py3-none-any.whl (135 kB)
|████████████…
-
My system possess intell i7 2700k with GPU RTX1060
My OS is Linuxmint 19.2 64bit, NVIDIA driver 435 with CUDA 10.1
Installed miniconda3 of python 3.8
it returns error... assuming its a python ve…
-
Hi all,
With the amazing rapid development and new versions I thought it best to check how you implement reproducible drug parameterization for research and publication, which might span 6-12 months …
-
In moving our GAFF residue template generators to http://github.com/choderalab/openmm-frocefields and updating them in the process, I'm trying to figure out how `simtk.openmm.app.ForceField` currently…
-
We would like to be able to execute OpenMM workloads, if possible, using QCEngine. This should involve creating a `qcengine.programs.model.ProgramHarness` subclass. Use the existing `*Harness` impleme…
-
**Major design decision**:
Currently, the charge method is handled on a "by system" basis; that is, as an argument to `createSystem`. So, all the components of a `System` are charged via the same m…
-
when creating an openmm system via `ForceField.create_openmm_system` the time required seems to drastically increase with MW. Currently I'm still waiting for MW ~900 molecule to finish after 30+min
…