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Add PTMA CGM3 IBI model to polyply library [10.1021/acs.macromol.3c00141] #279

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merged 13 commits into from
Oct 17, 2023

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ricalessandri
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Contributing the Iterative Boltzmann Inversion (IBI) CG model (that uses the same mapping as the Martini 3 model, a mapping dubbed "CGM3") developed for PTMA in https://arxiv.org/abs/2209.02072.

Test to follow, but first we need to figure out Discussion #278.

@ricalessandri ricalessandri added the parameter submission flag for submitting new parameters to the Martini polymer library label Oct 17, 2022
@fgrunewald fgrunewald added wait_for_vermouth This PR is waiting for new release of vermouth/martinize hacktoberfest-accepted labels Oct 18, 2022
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as mentioned in the discussions this PR needs some patching to the main code

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@ricalessandri the patching of the main code is done; with the current version on GitHub you should be able to add an info statement to your polymer on where to find the FF parameters. I suggest putting them on zenodo with a doi

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ricalessandri commented Jan 17, 2023

Great! Just waiting a bit more for the manuscript to finish peer review and then I'll act on this.

P.S. Should we remove the "wait_for_vermouth" label?

@fgrunewald fgrunewald removed the wait_for_vermouth This PR is waiting for new release of vermouth/martinize label Feb 7, 2023
@fgrunewald fgrunewald added the wait_for_publication can only be merged when paper is published label Jun 27, 2023
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@ricalessandri we are pushing the development of our RNA/DNA infrastructure. Before we are merging we are going to have one additional release and the probably a longer break for a couple of month. If you want this added into the release it has to be merged latest next week.

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OK, thanks for the heads-up!

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ricalessandri commented Aug 21, 2023

To Do:

  • update citation: 1dad7cc
  • add the non-bonded parameters (tabulated potential) via [ info ] in .ff file and Zenodo (enabled by this PR): 92d1803
  • add a test
  • add link to LIBRARY.md
  • add a line on the news section of the readme file to promote the paper

@ricalessandri ricalessandri changed the title Add PTMA CG IBI model to polyply library [arXiv:2209.02072] Add PTMA CGM3 IBI model to polyply library [arXiv:2209.02072] Aug 21, 2023
@ricalessandri ricalessandri self-assigned this Aug 23, 2023
@ricalessandri ricalessandri changed the title Add PTMA CGM3 IBI model to polyply library [arXiv:2209.02072] Add PTMA CGM3 IBI model to polyply library [10.1021/acs.macromol.3c00141] Aug 27, 2023
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@fgrunewald This is also done. Let me know if I missed anything and let me know if you like the news piece.

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@ricalessandri this PR looks mostly complete but there were two questions that came to my mind that we haven't discussed.

  1. I'm not a fan of adding two new ibi libraries but I also don't really see a way around it. I assume it becomes necessary because both residues are called PTMA.
  2. does the template generation actually work with the tabulated potentials?

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ricalessandri commented Oct 13, 2023

  1. As discussed, I renamed to ibi_cgm3 (lower-case). I think I did it in all the places it needed to be renamed.
  2. Yes, that works! This applies to Add PTMA GBNO2 IBI model to polyply library [10.1021/acs.macromol.3c00141]  #343, too

This is now ready to go!

One final comment I have, the [ info ] seems to get printed one time per monomer. A bit redundant but not sure if this can be prevented.

@fgrunewald fgrunewald merged commit dddbc16 into marrink-lab:master Oct 17, 2023
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@ricalessandri ricalessandri deleted the PTMA-CGM3-IBI-ff branch October 17, 2023 15:52
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