normal Is there any reference to make mapping file for lipid backmapping to CG

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1 year 6 days ago #7725 by tkim
Hello,

I am going to convert lipid structure from AA to CG. My model is not provided from Martini, so I need to do manually.

To do so, I need backmap file for the structure. It would be appreciated if I can reach any references to make mapping file. And can anyone enlighten me the difference between the linkers, GLY and AM? When can I apply each?

Thank you
Young

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1 year 6 days ago #7727 by riccardo
Hi Young,

First, one clarification. Usually, we call backmapping the inverse process (going from CG back to AA). So, you want to actually forward-map your AA lipid, i.e., you want to coarse-grain the lipid.

Have you followed the following tutorial?

cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5

may contain some more useful info.

I am not the lipid expert, so I'd wait for someone else to enlighten you on the GLY vs AM difference. In any case, you could already have a look at the lipidome ( cgmartini.nl/index.php/force-field-parameters/lipids ) and check whether a very similar lipid already exists and take it from there.

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1 year 5 days ago #7729 by tkim
Hi riccardo,

Thank you for your quick answer. Yes, you are right. This is like forward-mapping(?)

I found some literatures to distinguish the difference between GlY and AM. The lipid ,that I use, is with AM (sphingosine backbone). Based on this, I generated itp file using "lipid-martini-itp-v06.itp". and made a script for mapping.

Currently, simulation looks fine. Thank you again!

Young

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