Merge pull request #39 from openforcefield/2024-proteinprep-workshop

Add 2024 protein_prep workshop materials

Author: Yoshanuikabundi

source/workshops/2024/protein_prep.md

@@ -7,9 +7,33 @@ This workshop covers the preparation of a protein system from a structure downlo
 First session
 : [Feb 27 23:00 UTC](https://time.is/1000_28_Feb_2024_in_Canberra/Tokyo/Auckland,_New_Zealand/Los_Angeles/Chicago/Phoenix/New_York/UTC?Protein_Prep_OpenFF_Workshop)
 
+: [💨 Join on Zoom](https://us06web.zoom.us/j/84928391532?pwd=ZJoPVISZzA1LHo3mvfxbg1zug26Gas.1)
+
 Second Session
 : [Apr 17 12:00 UTC](https://time.is/2200_17_Apr_2024_in_Canberra/Beijing/Berlin/Los_Angeles/Chicago/Phoenix/New_York/London/UTC?Protein_Prep_OpenFF_Workshop)
 
 Zoom links will be published here 24 hours before the sessions begin.
 
-Materials and Google Colab links will be published here in advance of the workshop.
+Materials and Google Colab links can be found below.
+
+## Workshop Materials
+
+This workshop is a live demonstration designed to be followed along with on your own computer. The entire workshop can be executed in your browser without installing anything using Google Colab:
+
+[🤝 Protein Prep Workshop at Google Colab](https://colab.research.google.com/github/openforcefield/openff-docs/blob/main/source/workshops/2024/protein_prep/colab-protein_prep.ipynb)
+
+For better performance and to keep any artifacts produced, you can install the relevant software locally and execute the notebook there. This requires an installation of Mamba, Micromamba, or similar conda-forge compatible package manager (see [](/install.md)). First, download the workshop materials:
+
+[2024_protein_prep_workshop_materials.zip](path:protein_prep/2024_protein_prep_workshop_materials.zip)
+
+Extract the zip file and open a terminal in the extracted directory. Then, create the environment:
+
+```shell
+mamba env create -n protein_prep_workshop -f env.yml
+```
+
+And run Jupyter Lab in the new environment:
+
+```shell
+mamba run -n protein_prep_workshop jupyter-lab protein_prep.ipynb
+```

source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip

@@ -0,0 +1,34 @@
+name: 2024_protein_prep_workshop
+channels:
+    - conda-forge
+dependencies:
+    - ipywidgets=7.6.0
+    # Cookbook
+    - gitpython
+    - nbconvert
+    - nbformat
+    - requests
+    - packaging
+    # Examples
+    - openff-toolkit-examples>=0.15.2
+    - openff-interchange>=0.3.7
+    - openff-nagl
+    # - openff-bespokefit
+    # - openff-fragmenter
+    # - openff-qcsubmit
+    # - openff-recharge
+    - gromacs >=2021=nompi*
+    - lammps
+    - rich
+    - jax
+    - dgl
+    - nglview=3.0.3
+    - xtb-python
+    - pdbfixer
+    - mdtraj
+    - propka
+    - pdb2pqr
+    - openmmtools
+    - chemper
+    - dockstring
+    - mdanalysis