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Improving mapping files for GM1 and cardiolipin, and creating a mapping file for PIP2 #151

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ohsOllila opened this issue Sep 22, 2023 · 2 comments
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data mapping files, experiments, simulations

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@ohsOllila
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There are now quick and dirty mapping files added for GM1 and cardiolipin:

GM1: https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/mapping_files/mappingGM1charmm.yaml
related for example to this data: dx.doi.org/10.5281/zenodo.8331805
This works with other analyses except equilibration time analysis, but I think that there are some atoms still missing. Also the naming convention is not fully logical. This should be checked.

TOCL: https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/mapping_files/mappingTOCLcharmm.yaml
related for example to this data: dx.doi.org/10.5281/zenodo.8341624
This works, but the naming convention may not be logical.

In addition, a new mapping file is needed for PIP2 to include this data into the databank:
https://doi.org/10.5281/zenodo.8355310
This should be straightforward to do when starting from the existing ones for PI lipids:
https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/mapping_files/mappingSAPIcharmm.yaml
https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/mapping_files/mappingSLPIcharmm.yaml

@ohsOllila
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In addition, it seems that we need a mapping file for ceramide that is in this dataset: https://zenodo.org/record/8369427

This does not seem to the same ceramide that we already have which is N-palmitoyl-D-erythro-sphingosine (mapping file mappingCERcharmm.yaml).

@comcon1
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comcon1 commented Jul 18, 2024

TOCL is done as far as I know. We will do TMCL and TLCL mapping files because we are now obtaining experimental data for it. That part I will ask @ferdi385 to do.

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