There are multiple ways to generate topology for these ligands such as Prodrug, CharmmGUI, AcePype, and even AmberTools can also be used (get coordinates first, assign partial charges, and create topology).

If phosphatidic acid is part of membrane, you should search the CharmmGUI and get the relevent files, instead of creating from scratch.

Thank you sir, it is not the part of membrane it is a byproduct Ayaz Anwar

you can try ligpargen or swisparam webserver also.

i have generated it from Swissparam but there are errors coming from .itp file. Can you help sir? Harvinder Singh

I'll try at my end if you can sahre the structure of protein and smiles for your phosphatidic acid Tanusree Mookherjee