On Mon, Oct 16, 2023, Fadaei Fatemeh Mgr. via AMBER wrote:
>I am writing to seek your expertise in selecting the appropriate
>Amber force field for a circular DNA. I would like to use the Amber
>force field with the Gromacs package. I find myself torn between
>three options: amber99bsc1.ff.tgz, amber99sb_parmbsc0.ff.tgz, and
>amber14sb_OL15.ff.tar.gz. Since I am planning a long simulation, I want to
>ensure I choose the best force field for the job. I would also like to use
>the TIP3P water model.
I'm not the best expert on DNA force fields, but here is a try.
The current recommendation for Amber for DNA is OL21, but this may not be
supported by gromacs. To me, the amber14sb_OL15.ff (which combines protein
and DNA parameters) *sounds* like the best option, but I'm also not a
gromacs user. (You might ask on their help forums.)
For more info about DNA force fields, see this recent paper:
%A O. Love
%A R. Galindo-Murillo
%A M. Zgarbova
%A J. Sponer
%A P. Jurecka
%A T.E. Cheatham, III
%T Assessing the Current State of Amber Force Field Modifications for DNA-2023 Edition
%J J. Chem. Theory Comput.
%V 19
%P 4299-4307
%D 2023
Other options: (a) build the system in Amber, then convert the prmtop file
to gromacs format; (b) build and run the simulation in Amber.
...dac
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Received on Thu Oct 19 2023 - 09:00:04 PDT
