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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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Hi!
Would a public API make the reading of forcefield types and parameters easier?
Especially, what could be achieved by:
```
# import template generator
from openmmforcefie…
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To save storage space, it may be useful to extend `ForceField` to be able to read `.gz` compressed `ffxml` files.
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The "Foyer XML" files available within [Siepmann's website](http://trappe.oit.umn.edu/) for the TRAPPE-UA forcefield are incompatible with latest FOYER version 0.7.6.
**Code to reproduce behavior**…
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**Configuration:**
- RDKit Version: 2019.03.2
- Operating system: MacOS Mojave 10.14.6
- Python version (if relevant): Python 3.7.4
- Are you using conda? No
- If you are using conda, …
yy692 updated
4 years ago
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I was trying to parametrize a protein with a TPO residue, but I encountered an error. Could you please help me?
[protein_prep.txt](https://github.com/user-attachments/files/16683847/protein_prep.tx…
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While writing the code as per the [User's Guide](https://isicle.readthedocs.io/en/latest/user_guide/NMR.html) for NMR Chemical Shift Calculation in CREST Conformational Ensembles , there is a runtime…
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`ElasticMaker` shouldn't use submaker as default factory otherwise `chgnet` will be required to be installed as dependency
https://github.com/materialsproject/atomate2/blob/313f8098d58e3afcebd89…
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It seems forcefield_kwargs is not being propagated sometimes. I've fixed this error below by editing
```
File "openmmforcefields/generators/template_generators.py", line 1112, in generate_residue_t…