unanswered Martini 2.1P does not have "D" polarisable particles

  • Kusay
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2 years 3 months ago #9320 by Kusay
I am using the 2.1P martini FF for the system consisting of protein and DNA like GDP/ATP molecules

In martinize.py v2.5 I noticed that there no "D" polarisable particles for the 2.1P FF unlike the 2.2P FF, see example below:

2.2P FF:
"GLN": [spl("Nda D D"), [(0.400,5000), (0.280,None)], [], [], [(0.5,)]],
2.1P FF:
"GLN": [spl("P4"), [(0.400,5000)]],

This would indicate that these are no polarisable water-protein interactions in the 2.1P FF, why is that?

Doing a few, by no means extensive checks using gmx sigeps, the martini_v2.1P-dna.itp seems identical to the martini_v2.2P.itp

Would it be reasonable to martinize a system using the 2.2P FF and use the 2.1P.itp file (martini_v2.1P-dna.itp)?

A Martini 2.2P forcefield with the "T" tiny bead for DNA like molecules would be most ideal here, let me know if this exists

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