normal Adapt lipid topology from martini2 to martini3

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1 year 6 months ago #8956 by fralav
Hi,
I'm new to Martini and I would like to know how to adapt lipid topologies available for download from your lipidome section (for example cardiolipin) with the martini2 version, to the new martini3 version and whether it would be consistent the use of a martini2 itp for a lipid in combination with martini3 itps for other lipids in the same simulation.
thank you very much in advance!

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1 year 6 months ago - 1 year 6 months ago #8965 by riccardo
Replied by riccardo on topic Adapt lipid topology from martini2 to martini3
No, in general Martini 2 models are not compatible with Martini 3 ones. Some lipids are already available with the Martini 3 release (file "martini_v3.0.0_phospholipids_v1.itp"). You could get some inspiration from there + SI of Martini 3 paper to develop Martini 3 models for other lipids you are interested in. Maybe this tutorial can also be useful: www.cgmartini.nl/index.php/martini-3-tut...a-new-small-molecule

EDIT: I can't link the Twitter post directly (Invalid consumer key/secret in configuration), apparently, so I am copy-pasting it below.

Martini 3 lipids are a work in progress - see the post from Paulo (@SouzaPauloCT):
"To @Matth_Chavent, @sangyoung123go1 and others interested in Martini 3 and missing lipid parameters:

- cholesterol: we have beta model but demands more tests. We are considering pre-releasing a beta version, giving the high demand. The final version should be done in ~4-6 months.

- PIPs (new heads): pretty soon we should make the parameters available (thanks for the hard work of @MeloLab team). They will be published in a separate paper (if the reivewer like it :-)), but preprint and parameters should be avaiable pretty soon.

- GMs (new heads): It depends of sugars models, which are pretty advanced but still need some work. I guess, we will have available parameters in ~3-6 months. Hopefully, publication(s) will ready as well.

Be aware: full reparametrization of all lipids, including new tails, linkers and improvements in standard phospholipid heads are also in progress (right,
@CG_Martini and @jmelcr). But it will take some time (~1 year) to be ready. The plan is to publish them in a unique paper.

All tasks are potentially open for collaborations. You should look for
@CG_Martini or myself (@SouzaPauloCT) if you are interested in the taskforces."
Last edit: 1 year 6 months ago by riccardo. Reason: twitter post was not showing

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1 year 6 months ago #8969 by fralav
Thank you very much Riccardo for your quick reply.
I would have another question about the lipid tail mapping of some lipids.
For example, from the POPC mapping file I deduced, if I'm not wrong, that in the saturated tail 16:0, beads C1B and C4B are mapped 3:1 whereas C2B and C3B are mapped 4:1, but they correspond to the same atom type C1. Why the 3:1 mapped beads are not mapped with S bead type but both are regular?
Thanks a lot again

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