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Protonation in Martini3/martinize2
- liguo_UCAS
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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?
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?
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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