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OpenFF Forcecfield implementation #85

Merged
merged 11 commits into from
Jun 28, 2024
Merged

OpenFF Forcecfield implementation #85

merged 11 commits into from
Jun 28, 2024

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talagayev
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Changes made:

  • Upgraded OpenFF Toolkit to 0.16.0
  • Implemented OpenFF verion 2.2 to PDBFixer Path in OpenMMDL Setup
  • Added SMIRNOFF Template generator with OpenFF 2.2 in OpenMMDL Simulation scripts

@talagayev
Update forcefield_water.py
c76bd34 
Added Smirnoff Forcefield for small molecules
@talagayev
Update requirements.txt
5d0acb3 
Adjusted openff-toolkit version
@talagayev
Merge branch 'wolberlab:main' into forcecfield_implementation
1b30490
@talagayev
Update configurePdbFile.html
e5ff5e7 
Added the option to select small molecule force field
@talagayev
Update openmmdlsetup.py
fb5b2b5
@talagayev
Update forcefield_water.py
cece3a5 
Added OpenFF/SMIRNOFF Force field for small molecules
@talagayev
Update forcefield_water.py
45d890d 
Adjusted correct input
@talagayev
Update forcefield_water.py
6ceb8d5 
Updated OpenFF to 2.2 Version
@talagayev talagayev changed the title Forcecfield implementation OpenFF Forcecfield implementation Jun 6, 2024
@talagayev talagayev linked an issue Jun 6, 2024 that may be closed by this pull request
[WIP] Implement Additional Small Molecule Forcefields #76
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@talagayev
Update openmmdlanalysis.py
453e9a7 
Error fix, due to this file being default svg instead of png
@talagayev
Update openmmdlanalysis.py
df1e1a8 
fixed error with ligand numbering figure, due to type
@talagayev
Merge branch 'wolberlab:main' into forcecfield_implementation
e90bdf7
@sheng19331
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Hi
Thanks for the great tool and update. But i still haven't found the option of openFF in the GUI of OPENMMDL-SETUP. Do I need to implement this FF by modifying the script?

@talagayev
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Hey @sheng19331,

I think it was because of the OpenFF option being in my OpenMMDL Github repository, since it is currently not merged and probably that was the reason why it was not accessable.

I would merge it now with the development branch of OpenMMDL, so that when you download the development branch (I am not sure if it would work with git clone, else just download it through selecting the Development_v_1.1 branch and then Downloading the Zip File) and do the installation there with pip install and then it should work.

This should work, if it didn't glad to help :)

@talagayev talagayev merged commit c1a2c6d into wolberlab:Development_v_1.1 Jun 28, 2024
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[WIP] Implement Additional Small Molecule Forcefields
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@talagayev @sheng19331