GROMACS version: 2020.4
GROMACS modification: No
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I am trying to generate a system of small molecules in organic solvents. I generated my parameters using the Jorgenson groups’ LigParGen software, and I made a box using packmol. I am not sure where to go from here. I was hoping for guidance or a tutorial. I am really new to this and the manual is kind of confusing.
I tried using pdb2gmx to convert the box.pdb I generated in packmol into a .gro file. Despite having the .itp files for the molecules in the CWD, Gromacs could not find the molecules. “‘molecule_name’ not found in residue topology database” I also tried making a sub-directory in the CWD named “system.ff” but that was not recognized either. This was true regardless of whether or not I indicated -ff in my pdb2gmx command or not. I would appreciate any guidance with this as I am just learning how to use the program in this way.