Amber94 for protein-DNA complexes

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1

GROMACS version: 5.0
GROMACS modification: Yes/No
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Hey there!
I am currently running molecular dynamics simulations on a protein-DNA complex to further investigate DNA bending. For this purpose I am using the GROMACS simulation package and the AMBER force field included in this package: AMBER99SB-ILDN for protein and AMBER94 for nucleic acids. After further research, I now found out that simulating DNA is more complicated and improved force fields like parmbsc0 or parmbsc1 are used more frequently for the analysis of protein-DNA complexes.

I am now dealing with the question if it makes sense to use the output trajectories of the simulations using the AMBER94 force field, or if the output will not be accurate enough? Could you give me some assessment regarding this issue and the differences of the output generated when using old force fields?

Thanks a lot in advance!

2

AMBER94 is entirely unreliable. Your DNA is probably going to fall apart. You need a modern force field.

3

thanks for your reply