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Adding CA ions to parsing list - proteincomponent.py #265

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merged 7 commits into from
Apr 17, 2024
Merged

Adding CA ions to parsing list - proteincomponent.py #265

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52ab413
Addin CA ions to parsing list - proteincomponent.py
RiesBen Jan 13, 2024
fa999de
Update proteincomponent.py
RiesBen Jan 13, 2024
df08da1
fix summation of bonds for charge calculation
richardjgowers Apr 11, 2024
decd445
Update proteincomponent.py
richardjgowers Apr 16, 2024
1827ecc
protein loading: add some more common ions
richardjgowers Apr 17, 2024
3b530bd
protein loading: be a bit more permissive on ion names
richardjgowers Apr 17, 2024
4cc370e
protein loading: review comments
richardjgowers Apr 17, 2024
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4 changes: 2 additions & 2 deletions gufe/components/proteincomponent.py
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Expand Up @@ -51,8 +51,8 @@
}


negative_ions = ["F", "CL", "Br", "I"]
positive_ions = ["NA", "MG", "ZN"]
negative_ions = ["F", "CL", "BR", "I"]
positive_ions = ["NA", "MG", "CA", "ZN"]
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Would it make sense to just add every mono and divalent ions that are defined in the AMBER ffxml?

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We're probably replacing this entirely soon, so a small fix is ok for now. I'd be more interested in a test to encode the fix/behaviour



class ProteinComponent(ExplicitMoleculeComponent):
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