amino acid modification with additional beasd

[csbrasnett]

is it possible to have a modification that adds an additional bead to the given residue? Eg. if we have a phosphoserine, we can't give a single letter aa code in a fasta file, but could use the -mod flag to change, but this would require us to add a second bead to the side chain in addition to the one that's already there. Ideally we'd have something like:

[modification]
pser
[atoms]
BB {resname: "pser", replace :{'resname': ser'}
sc1 {resname: "pser", replace :{'resname': ser'}
sc2 {resname: "pser"}
[links]
sc2 sc1 1 1 1000

but I don't think that's what the syntax would look like

[fgrunewald]

@csbrasnett in principle it should be possible but there are some caveats. You cannot simply insert a node in a meta-molecule molecule. You'd have to modify the molecule and then rebuild the meta-molecule. But still the new particles would end-up in the end of the itp file unless you reorder the molecule before writing. The GoProcessor in vermouth is an example on how to setup this kind of functionality.

@pckroon how are we doing this in martinize2? I think it is currently not possible.

[pckroon]

@pckroon how are we doing this in martinize2? I think it is currently not possible.

Sure it is:

[modification]
pser
[atoms]
BB {"resname": "pser", "replace" : {'resname': ser'}
sc1 {"resname": "pser", "replace": {'resname': ser'}
sc2 {"resname": "pser", "PTM_atom": true, "atype": ...}
[edges]  ; bonds maybe?
sc2 sc1 1 1 1000
BB sc1

Getting coordinates is a separate problem.