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.
From what I have understood is that this ffMOL.itp would have the non-bonded parameters with the sigma and epsilon values and in case while using cgenff there is no sigma and epsilon value printed out. And moreover most of the sigma and epsilon values for various atomtypes are not present in ffnonobonded.itp in the mutated force field for charmm36? Would it be wise to use the sigma and epsilon values from the regular force field for the atomtypes definition in the ffMOL.itp file?
cgenff atomtypes are in the ffnonbonded.itp
If you are not finding an atom parameter in some version of charmm36, it might be that this ff version is older than the one used to parameterize the ligand.
I guess it will be just fine if I call the force field in the top file which would indicate it towards the ffnonbonded.itp file and thereby reading the atomtypes in the process. or do I have to explicitly declare the atomtypes in ffMOL.itp or ffmerged.itp in that case as the way you have done?
If the atom description is the ffnonbonded.itp, then including force field will suffice. For dummy atoms you will likely still need to include an additional .itp file.