unanswered Martinize2 not recognizing sugar residues

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1 year 3 months ago #9597 by VBurns
Hi everyone,

I'm new to martini so bear with me. I've been trying to use the martinize2 tool to get CG starting files from a pdb containing mAb (protein) and sugars in it. It's able to figure out the protein, but it is not recognizing the sugars residue names, and so it deletes the whole molecule (as hey are bound to the protein). I have downloaded the PARAMETERS.itp files but I can't find anywhere how to add them into the martinize2 command line and based on the .ff files from the martinize2 github, it does not seem like it has the sugars.ff in it. Any ideas as to how I can tackle this?

Thank you.

Violetta

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