Wednesday, March 24, 2021

NMRlipids IVb: Toward submission of the manuscript with PE and PG results (2)

The manuscript is now substantially updated based on comments to the previous post and discussions in the online meeting held on 12th of January 2021. All force field evaluations are moved to the supplementary information, analysis of lipid structures from PDB is improved, illustration of similar structures of different lipids bound to different proteins is added to figure 4, and dihedral distributions in figures 2 and 3 are changed to relative energies in kT units. 

I believe that the manuscript is close to the submission stage, and I would like to submit it within one month from now, i.e., before 24th of April 2021. Therefore, the last opportunities to comment the manuscript are approaching. 

Before the submission, the figures 1 and S1-S3, and experimental and simulation details needs to be polished. 

We also need a good title for the article. The title is discussed in this issue.

In addition to these issues, I would be happy to have any comments on the manuscript as soon as possible, particularly if you have major comments on the content of the manuscript.

3 comments:

  1. We have recently (motivated by the first NMRlipids paper from 2015) updated Slipids force field (Slipids-2020) with new torsional parameters for the headgroup region: J. Phys. Chem. B 2020, 124, 40, 8784–8793. Trajectories for DMPC, DPPC and POPC are uploaded to Zenodo (10.5281/zenodo.4573980, 10.5281/zenodo.4573282 , 10.5281/zenodo.4573315 )

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  2. Hi Alexander, thank you for the contribution! Would you happen to have any trajectories with the new parameters for PE (or PG)? It would be great to include these in the PE/PG force field comparisons that we are just now wrapping up.

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  3. Hi Marcus,
    Not yet, a bit busy right now but really it would be nice to have them... In principle setup is rather straightforward with available .itp and .pdb files for these lipids

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