I want to create a binary aqueous mixture with DMSO using opls forcefield Since a simple pdb file for DMSO coordinates won't work by input into pdb2gmx, topology files have to be created. What are the steps to be followed for creation of .itp files for DMSO? If I use software like TopolGen or mktop, what changes do I have to make in the files generated? From where do I fill out certain missing information?
To generate parameters for a new molecule in an existing force field, you need to familiarize yourself with the parametrization protocols of that force field. For OPLS, this typically involves some QM calculations for charge assignment and bonded parameters based on relative energies in the gas phase; empirical refinement follows based on liquid properties.
A DMSO model already exists in OPLS-AA in GROMACS, though, so I don't understand your assertion that it doesn't work. The residue is clearly labeled "DMSO" in aminoacids.rtp but does have a cautionary note about the fact that the parameters are not thoroughly validated. But perhaps those can be a starting point for additional optimization, to save you some of the laborious work of coming up with parameters de novo.
Use pdb2gmx sub program in Gromacs. If you need OPLS all atom force field parameters select 15 as I remember.
Anyways DMSO is a critical solvent. There are research papers published just only for optimization of force filed parameters of DMSO. Please refer those articles for more information.
Since DMSO is a simple molecule, I recommend you building the ITP file manually. For this, you must take into account the characteristics of atoms in the force field that you use. I consider that there is no preset protocol, since in these cases you must solve timely absences, such parameters forces between atoms not considered by the force field.
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