normal Leucine Bead type AC1 or C1

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8 years 5 months ago #5143 by flaviyan
Leucine Bead type AC1 or C1 was created by flaviyan
Dear Moderators,

I noticed in the martinize.py tool the LEU and ILE bead types are

AC1 (for -ff martini21 or martini22)
C1 (for -ff martini21p, martini22p, elnedyn, elnedyn22, elnedyn22p).

I looked into the literature and can't find the explanation for the different bead type with the different force fields.

The AC1 bead type definition says:
; AMINO ACIDS (required for Q-C interactions inside proteins)
AC2 72.0 0.000 A 0.0 0.0
AC1 72.0 0.000 A 0.0 0.0

is it that the martini21p, martini22p, elnedyn, elnedyn22, elnedyn22p can account for the Q-C interaction with just the C1 bead type?

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8 years 5 months ago #5146 by djurre
Replied by djurre on topic Leucine Bead type AC1 or C1
The difference between C1 and AC1 lies in how they interact with charged particles: they \sigma for C1-Q* interactions is 0.62 nm, for AC1-Q* is 0.47. This change back to 0.47 nm was introduced in the martini 21 forcefield for Proteins and remains in the martini 2.2 version (martini21 or martini22).

For the polarized forcefields this change was no longer needed, hence AC1=C1 (martini21p, martini22p, elnedyn22p).

For Elnedyn the change was never introduced in the first place and there is only C1 (elnedyn, elnedyn22). (This is one of the many subtle differences between Elnedyn and Martini that make the Martini protein forcefields so difficult to maintain).

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