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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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mapping for nucleobases #420

Closed supremesquishy closed 2 years ago

supremesquishy commented 2 years ago

Hello Martinize2-Developer Team,

I want to parametrize a small molecule GDP in a consistent manner with the martini3 ff. There is a topology file for nucleobases martini_v3.0.0_nucleobases_v1.itp but I can't find anywhere mappings for them.

Are they somewhere available? If not is it possible that you can share them with me?

Thank you in advance.

fgrunewald commented 2 years ago

Hi @supremesquishy,

Nucelobase parameters and mappings remain unpublished for the time being. Therefore we cannot distribute or provide mapping parameters for the nucleobases or DNA via martinize2. You will need to file a request with the corresponding author(s) of the Martini3 paper. We are aware that this is a less than ideal situation, however, as martinize2 developers our hands are tied in this regard.

Cheers, Fabian