Dear gromacs users,
I am working on a simulation of a gold-nanoparticle assembly with a supramolecular complex to study host-guest encapsulation process. I prepared the gold nanoparticle assembly structure with -CH2-NH3+ ligands in charmm-gui and obtained the parameters. I need to modify the ligand to add phenyl rings to NH2 group which I did using pymol. But how do I obtain the forcefield parameters for the newly introduced phenyl moiety in the nanoparticle assembly. I already obtained the parameter for the structure without the phenyl ring from charmm-gui.
Can I remove the phenyl ring and cap it with hydrogen and separately generate its parameters using cgenff or some other servers and then just add them back in the actual topology file of the molecule?
Any help is much appreciated, thank you