Many Markush structures have more than one R-group attached to them. Therefore, the R-groups are commonly assigned indices, as in 'R 1 or 'R 2 '. When creating SMILES strings with R-group representations, this leads to the introduction of tokens with multiple meanings. For example, the token '1' in the SMILES string 'c1ccccc1[R1]' can represent a ring opening or closure or an R-group index. To evaluate the influence of this potential problem, the performance of two models was compared.