Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do:
Getting forcefield parameters: Your question is about this, so I will give a detailed explanation. There are many forcefields to choose from, e.g. MMFF94, UFF, CgenFF, GAFF, OPLS-AA etc. Which one you use depends on what you are trying to study. Some general forcefields have been parameterized to be compatible with protein force fields, for example CgenFF with CHARMM36, GAFF with Amber as you can probably guess. I am by no means an expert on this topic, so I will advise you to look through the literature for which force field (or combination) will suit your purpose the best.
Getting parameters in a gromacs compatible format can also be tricky. There is a guide on how to do that with some popular forcefields here. For the sake of being a complete answer, I will summarize the information briefly:
- GAFF - You can use Antechamber with the python module acpype (which has been mentioned in the other answer) to generate gromacs compatible topology files.
- CHARMM - For this you can use the CgenFF official website (https://cgenff.umaryland.edu/) or as it was known earlier, paramchem.org. This site produces parameters in the form of .str files which have to converted to gromacs compatible format using the cgenff_charmm2gmx.py python script which is available here.
- GROMOS - ATB can generate gromacs compatible files.
- OPLS-AA - The LigParGen server from Jorgensen group produces gromacs compatible files.
There is also another server called swissparam which can generate parameters for small molecules, however it takes most of the bonding and charge parameters from Merck Molecular Force Field, and Van der Waals parameters from CHARMM22. The parameters are supposed to be compatible with CHARMM protein forcefield, but I have never used it with a protein so I can't be sure.
Running the simulations: In the question you have written that you already have a topology file. For other readers of this answer, a standard gromacs topology file would look like this:
; Include forcefield parameters
#include "charmm36-jul2020.ff/forcefield.itp"
; Include small molecule parameters
#include "ligand.itp"
; Include TIP3P water topology
#include "charmm36-jul2020.ff/tip3p.itp"
;Include topology for ions
#include "charmm36-jul2020.ff/ions.itp"
[ system ]
;Name
small molecules
[ molecules ]
; Compound #mols
LIG 1
Here I have named the small molecule (in your case benzene) as LIG, and its parameters are stored in the ligand.itp file (which you can get from swissparam, or after converting the str file from CgenFF website).
Also note that you don't always need to include the original forcefield parameter files as you have done in the question. If the .itp files say that the "parameters were taken" that means they are already present in the .itp files. However, different forcefields use different combining rules, which are defined in the forcefield.itp for that forcefield, so it has to be included. In my case, I included the ion and tip3p water topolgy because I needed them later. The forcefield.itp is also required for the tip3p water parameters.
After you have the topology and parameters, you can then run gromacs as usual.
