On Thu, Apr 10, 2025, Rahul Singal via AMBER wrote:
>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).
We would need to see the input PDB file you gave to antechamber. The "fix"
should not be to have to manually edit the atom types. Rather, one needs to
understand why antechamber thought that there was only one atom bonded to
O3' in the first place.
....regards....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 11 2025 - 10:00:02 PDT
