Difficulty Replicating Antibody Optimization Results

[benyaminjami]

I've been trying to replicate the antibody optimization results detailed in the paper, strictly adhering to the provided instructions and ensuring the activation of OpenMM relaxation. However, my attempts to reproduce the expected outcomes have not been successful. According to the paper, the average ddG calculated by GNN predictor should be approximately -7, but my results consistently show an average ddG of around -4, even when num_residue_changes is set to 0.