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

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2 months 1 week ago #7725 by tkim
tkim created the topic: Is there any reference to make mapping file for lipid backmapping to CG
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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2 months 1 week ago #7727 by riccardo
riccardo replied the topic: Is there any reference to make mapping file for lipid backmapping to CG
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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2 months 1 week ago #7729 by tkim
tkim replied the topic: Is there any reference to make mapping file for lipid backmapping to CG
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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