I have a small molecule, 4-aminopthalimide with a purely aliphatic group attached to its terminal end, that I want to use for MD in a CHARMM-GUI made lipid membrane, using GROMACS.
I optimised the structure on HF/6-31G* using ORCA, and then used the CGenFF server to get the Charmm36 compatible .str file during which I get ~20 penalty values on charges, and high (>50) penalty values on dihedrals of the ringed structure.
I tried using the ffparam-gui (with psi4 for QM and OpenMM for MM) to optimise the parameters. I am unable to optimise the dihedrals, due to some issues arising from the bonds to be parametrized being part of the ring preventing psi4 from being able to run PES scans.
I have attached the initial .str file as obtained from the CGenFF server, as well as the .mol2 file of my molecule. 4apC9.mol24apc9.str
Since the majority of the issues seem concentrated in the ringed structure, I tried to parametrize the molecule without the aliphatic chain. While charge parametrization seems to have worked, the dihedral issue still remains. (Also, is there any way to validate these charges?)
Is there a better way to go about this? Kindly help. (I don't have access to Gaussian or a CHARMM license, yet.)