DNA-protein sims in MARTINI 3

[agoliaei]

Hi,
Thank you all for sharing your work with the community!
I think I have confused myself a little bit, so I decided to reach out and ask for help. Is it possible to do CGed DNA-protein simulations using MARTINI 3 parameters? I see there is an itp file in here: martini_v300.zip, but I don't see any mappings.
If this is not the right place for this question please tell me.
I appreciate your help.

[pckroon]

Unfortunately, afaik there are 2 issues:

1. there are no links defining the bonds/connections/parameters between the protein and DNA parts. This does not matter if the same system contains DNA and protein molecules separately, and if you have a DNA/protein chimera you can always add the links yourself.
2. The CLI only lets you specify elastic network parameters for the entire system, and as far as I know they should be different for DNA and proteins.

@fgrunewald do you know of a workaround?

[fgrunewald]

@agoliaei Martini3 DNA is currently not available; we're working hard on finalizing the model but I cannot make any predictions when this model is released.

[agoliaei]

Thanks so much for clarifying. I appreciate it.