Ligand topolgies for pmx

Hello all,
Can anyone give me an insight on the ffMOL.itp file which contains the (van der waals parameters) provided in the files in the Github page in Prot_lig benchmark. How does one create such a file, I mean while using the ligandHybrid.py script I don’t come across the need for invocation of ffMOL.itp file.
Moreover when one gets the merged.itp file from ligandHybrid.py how does one go about build the top_water.top and top_protein.top file?

ffMOL.itp were generated at the ligand parameterization step. There I create MOL.itp with atoms, bonds, angles, dihedrals and ffMOL.itp with atomtypes. This separation is not strictly necessary, but I find it convenient, as later, when creating ligand hybrids, I can add new dummy definitions into ffMOL.itp.

Vytas

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