To establish an efficient way to utilize a gap mode plasmon in flocculates of MNPs, under external and ATR configurations, we controlled interaction between adsorbed species and metal nanostructures. We have successfully formed flocculates of AgNPs using electrostatic interaction between dissociated PMBA (-COO-), protonated PATP (-NH3+) and counter ions (Mn+, X-), as well as van der Waals force between neutral PMBAs (-COOH) and PATP (-NH2) on AgNPs. Detailed adsorbed state of PMBA and PATP as well as trapped counter ions were characterized using enormous SERS enhancement in flocculation-SERS. In a gap mode under an external geometry, most of thiol molecules on Ag films immobilized AgNPs through van der Waals force and electrostatic interaction. They showed similar Raman enhancement of 108-109, in accordance with those predicted by FDTD calculations. Only thiols with tert-methyl group did not immobilize any AgNPs due to steric hindrance. In a gap mode under ATR configuration, additional enhancement was obtained by a coupling of PSP and a gap mode.