normal Caffeine .itp file

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4 weeks 1 day ago #9143 by JBinder
Caffeine .itp file was created by JBinder
Hello Martini fans,

is there any way to obtain the caffeine .itp file used by Mr. Souza in the following paper?
www.nature.com/articles/s41467-020-17437-5

I can find the bead mapping in the sups but nothing more.

Thanks a lot for your help and keep up the great work

Jonas

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4 weeks 1 day ago #9145 by riccardo
Replied by riccardo on topic Caffeine .itp file
Hi Jonas,

We recently released a set of 90 small molecule models that you can find at that repo ( github.com/ricalessandri/Martini3-small-...all_molecules_v1.itp ) and that are described in this preprint:
doi.org/10.33774/chemrxiv-2021-1qmq9

As part of that set, you can find the caffeine model:
github.com/ricalessandri/Martini3-small-...lecules_v1.itp#L2034

Note that besides that "collection" file, the repo contains several files for each molecule, that is, not only the itp but also the AA-to-CG mapping file, etc (AA=all-atom; CG=coarse-grained). Take a look here for a description of all the files available for each molecule:
github.com/ricalessandri/Martini3-small-...les/tree/main/models
and feel free to follow up here if something isn't clear.

For example, for caffeine you can find the itp for the single caffeine at:
github.com/ricalessandri/Martini3-small-...ps/opt-poly/CAFF.itp
the gro file at:
github.com/ricalessandri/Martini3-small-...models/gros/CAFF.gro
etc.

Cheers,
Riccardo

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4 weeks 1 day ago #9146 by JBinder
Replied by JBinder on topic Caffeine .itp file
Hi riccardo,
thanks a lot for this quick and very thorough answer.

I will take a look at it!

Best regards
Jonas

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