normal backward with POPE and POPS

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4 months 3 days ago - 3 months 4 weeks ago #7999 by soltak
backward with POPE and POPS was created by soltak
I am trying to backward a POPE/POPS lipid bilayer to charmm36, but couldn't find the mapping files. Could anyone provide me the mapping files? Thanks!

Yong Wang
Postdoc in Lindorff-Larsen Lab
Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science
Department of Biology, University of Copenhagen
Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
Last edit: 3 months 4 weeks ago by soltak. Reason: typos

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3 months 4 weeks ago #8007 by bart
Replied by bart on topic backward with POPE and POPS
To my understanding only some example backward files were provided. In the backward paper and this tutorial , you can find how to create your own mapping files.

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3 months 4 weeks ago - 3 months 4 weeks ago #8008 by riccardo
Replied by riccardo on topic backward with POPE and POPS
Indeed. Make sure to also check the lipidome ( cgmartini.nl/index.php/force-field-parameters/lipids ). Some mapping files may be there but not in the backward "Mapping" directory. I quickly checked for POPE and POPS and found indeed no mapping files, e.g., see POPE at cgmartini.nl/index.php/force-field-param...ml?dir=PE&lipid=POPE
Last edit: 3 months 4 weeks ago by riccardo.

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3 months 4 weeks ago #8009 by soltak
Replied by soltak on topic backward with POPE and POPS
Thanks a lot for your reply, both Riccardo and Bart.

Yeah, I do find some mapping files, e.g. for POPC, but not for POPE and POPS. Alright, I will follow the tutorial and make my own mapping files. Thanks!

Yong

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3 months 4 weeks ago #8010 by tsjerk
Replied by tsjerk on topic backward with POPE and POPS
Have you checked the repository on Github ( www.github.com/Tsjerk/Backward )? The mappings for these lipids should are already available.

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3 months 4 weeks ago #8011 by soltak
Replied by soltak on topic backward with POPE and POPS
Woo! Fantastic. Sorry, I didn't check the github version. I thought it is the same version as the one from the cgmartini website. Yes, the mapping files for both POPE and POPS are there. Thank you so much, Tsjerk!
Issue closed!

Yong

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3 months 2 weeks ago #8028 by bart
Replied by bart on topic backward with POPE and POPS
I did not know about the mapping files available on github and I will see if we can merge these databases or at least link to it in a clear manner.

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