Alzheimer´s disease is a neurodegenerative disorder affecting more than 34 million people worldwide and is postulated to be caused by an abnormal accumulation of Aβ-amyloid plaques. The Aβ-amyloid plaques consist of misfolded peptides, which leads to the plaques exhibiting multiple possible morphologies. One way of studying these polymorphic Aβ-amyloid fibrils is by using different ligands with affinity for Aβamyloid fibrils. The purpose of this report was to evaluate whether the in silico based method ab initio molecular docking can be used to accurately predict amyloid-ligand interactions. The molecular docking method was evaluated by assessing its ability to reproduce experimentally derived relative binding affinities and reproducing conformations of amyloid-ligand complexes. The results indicate several complications of the ab initio molecular docking in performing the mentioned tasks. However, some modifications to the protocol used in this report might possibly improve the performance of the method.