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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