Post translational modification

[amiel-ab]

Hi all,

I am trying to add post translationnal modification that is a palmitoyl chain to a lysine from a protein, in CG (Martini3).
@fgrunewald advised me to use lipidation parameters from here https://pubmed.ncbi.nlm.nih.gov/38019969/
However, their lipidation parameters are about cysteine-palmitoyl but not lysine-palmitoyl.

Do you have any idea on how i could use polyply to generate such modified structure?

Thank you for your consideration.

[fgrunewald]

@amiel-ab,

My recommendation would be to build an all-atom model of your lipidation using the CHARMM-GUI. Subsequnetly, we can show you how the martinize2 files can be adopted to generate coordinates and input files for your protein. Please note that for this purpose I will later transfer the discussion from the polyply to the martinize2 GitHub page.

Just reply to the issue once you obtained the all-atom structure

Cheers,
Fabian

[amiel-ab]

Ok it is working fine, Thank you very much Peter for your help and patience !

[amiel-ab]

for the link i thin k it worked ; just to be sure in my case i have two residues LSP may i have one sep.ff and sep2.ff files ?

[pckroon]

Not sure I understand what you mean by that. In general there is no requirement to keep things in one file though.

[amiel-ab]

I mean i have two LSPs one that got GLY before and SER after and one that got GLY before and ARG after so this should need two sep.ff no ?

[pckroon]

I don't think so, since LSP will be LSP, right? And if you define your links as connecting to $protein_residues you also need only 2 (or even 1) link.