We investigate the van der Waals interaction of D,L-Ala cyclopeptide nanotubes and various ions, ion-water clusters and C(60) fullerenes, using the Lennard-Jones potential and a continuum approach which assumes that the atoms are smeared over the peptide nanotube providing an average atomic density. Our results predict that Li(+), Na(+), Rb(+) and Cl(-) ions and ion-water clusters are accepted into peptide nanotubes of 8.5 Å internal diameter whereas the C(60) molecule is rejected. The model indicates that the C(60) molecule is accepted into peptide nanotubes of 13 Å internal diameter, suggesting that the interaction energy depends on the size of the molecule and the internal diameter of the peptide nanotube. This result may be useful for the design of peptide nanotubes for drug delivery applications. Further, we also find that the ions prefer a position inside the peptide ring where the energy is minimum. In contrast, Li(+)-water clusters prefer to be in the space between each peptide ring.