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OpenMM's topology objects and readers/writers don't provide enough chemical information to actually parameterize small molecules nonstandard biopolymers, post-translational modifications, glycosylatio…
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It would be really helpful for purposes of fully documenting a calculation if TransRot were to create a table of all of the pairwise interaction potential parameters used in the simulation, including …
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Using 1ctf as an example:
```python
structure = ampal.load_pdb("/Users/leo/Documents/code/aposteriori/tests/testing_files/pdb_files/1ctf.pdb")
for atom in structure.get_atoms():
…
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Hi all!
I'm opening this issue so we can discuss about how we could implement MARS in Npgsql.
@bricelam gave us a heads up about the requirement of MARS by Entity Framework 7. https://github.com/npg…
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In #357 we decided to use distance cutoffs as a proxy for determining 1-3 and 1-4 pairing.
A more precise way to determine this is using the adjacency matrix described in that issue. The implementati…
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### Problem
I need to extract the overall dimensions and centre of each cavity so that I can give them to Autodoc Vina for docking a ligand. An easy way would be to export to "cavity.pdb", then parse…
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### Steps to reproduce the issue
```console
$ spack spec -I cp2k+cosma+libvori+mpi_f08+pexsi+plumed+pytorch+quip+sirius+spglib+ipo+elpa+dlaf+openmp build_system=cmake lmax=7 ^cosma+shared ^cmake/v…
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In https://github.com/Materials-Consortia/optimade-python-tools/pull/986 I have proposed two additional requirements for formulas (`chemical_formula_reduced`, `chemical_formula_hill` and `chemical_for…
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**Problem description**
@HuubAppelboom raised an issue in today's SimSwap... - [meeting](https://wiki.camaraproject.org/pages/viewpage.action?pageId=34734375)
> @HuubAppelboom raised a good point …
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Patches are meant to fix https://github.com/phetsims/scenery/issues/1643.
It would be good to quickly test with Firefox 128+ on all links with ?locale=ar (or dynamic locale => Arabic if possible), al…