Dear AMBER Community,
I am currently working on parameterizing FRET probes (tCo and tCNitro) using GAFF via Antechamber.
During the process, I encountered an issue with the atom typing:
The O3' atom, which is an oxygen with a negative charge, is being assigned the atom type "o" (for carbonyl oxygen), whereas it should ideally be assigned as "os" (for a single-bonded spł oxygen like in hydroxyl or ether groups).
I have attempted to manually correct the atom type in the mol2 file and proceed with the rest of the workflow. However, doing this introduces additional problems, such as incorrect torsion parameters, and the resulting parameters do not behave as expected in simulations.
Has anyone faced a similar issue or can suggest a recommended way to:
1.
Ensure the correct atom type assignment (e.g., force Antechamber to use "os"),
2.
Or, safely correct this post-hoc without introducing inconsistencies in torsion/angle definitions?
Any suggestions or insights would be greatly appreciated.
Best regards,
Rahul Singal
Undergraduate Student
IIIT Hyderabad
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Received on Thu Apr 10 2025 - 11:00:03 PDT
