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Hi,
I am building modified nucleic acid topology using modXNA approach, thanks to the earlier suggestions.
As I plan to run simulations in Gromacs, I am converting AMBER prmtop to Gromacs topology using Parmed. and add these parameters to ff port from
https://github.com/srnas/ff/tree/master/amber_na.ff
I realized Parmed converted topology (for rU) follows C6-N1-C1'-O4' for chi angle and values are same as chiOL3 paper.
(I understand this is not AMBER related issue) but amber_chiOL3 ff from GitHub follows conventional O4'-C1'-N1-C6 with special define sections, still with the same chiOL3 values.
Could expert suggest what is the correct order of atoms if simulations are supposed to be run in Gromacs?
Thanks in advance,
Mandar
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Received on Tue Jan 13 2026 - 04:00:11 PST
