I am new to MD / gromacs and I am trying to use MD not for biological system but for generic materials science. Specifically, I am trying to simulate the interaction between hydrophobic molecules (perfluorodecane) and water molecules.

I've downloaded multiple files from ATB for my molecule perfluorodecane, and the files are as below:

files for united atoms:

7CKR_unitedatom_original_geometry.itp

LYG3_GROMACS_G54A7FF_unitedatom.pdb

files for all-atoms:

LYG3_allatom_optimised_geometry.pdb

LYG3_GROMACS_G54A7FF_allatom.itp

Updates for force field:

gromos54a7_atb.ff.tar.gz, which I uncompressed to my local directory.

To conduct MD, I believe I need to make a topology file, i.e., pfd.top. I tried to make it using pdb2gmx. pdb2gmx asks me which force field I want to use, and I chose #1, which is the updated gromos54a7 force field that I created using the tar.gz file listed above.

I followed those steps twice, once for united atoms and once for all atoms, and for both attempts, I got the error message of

'Residue '7CKR' not found in residue topology database'

or

'Residue 'LYG3' not found in residue topology database'

Could you please advise me how to resolve this issue? I can spend as many hours as needed, so just let me know the right direction.