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normal Protonation in Martini3/martinize2

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1 year 7 months ago #9488 by liguo_UCAS
Protonation in Martini3/martinize2 was created by liguo_UCAS
In the literature(Protein–ligand binding with the coarse-grained Martini model doi.org/10.1038/s41467-020-17437-5), I found the amino acid protonation could be changed in Martini3 (Like ASP45 was kept neutral). But I didn't figure out how to achieve this:

In martize2, the blocks and modification don't contain the neutral state of amino acids. Though an example in option -modify is "Add a modification to a residue. Desired modification is specified as, e.g. A-ASP45:ASP0",
Matinize2 will issue the error: "WARNING - unmapped-atom - Can't find modification mappings for the modifications ".

Do we need to change the side chain particle type from Q to P/N like in Martini2 by hand?

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1 year 7 months ago - 1 year 7 months ago #9489 by liguo_UCAS
Replied by liguo_UCAS on topic Protonation in Martini3/martinize2
In the vermouth-martinize github ( github.com/marrink-lab/vermouth-martiniz...ni3001/aminoacids.ff ), I found the Martini3001 aminoacids.ff had been updated to contain the neutral state of ASP/GLU/LYS/ARG. But it seems this change hasn't been used in martinize2?
And this updated martini3001 ff file seems not be offered on this weibsite?
Last edit: 1 year 7 months ago by liguo_UCAS.

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  1. Force Fields
  3. Proteins
  5. Protonation in Martini3/martinize2
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