I am afraid that there may be an error in your Grantham Score matrix defined in your script.
According to the describtion of Grantham Score (https://ionreporter.thermofisher.com/ionreporter/help/GUID-D9DFB21C-652D-4F95-8132-A0C442F6
Thanks for your question.
This matrix was built based on the reference "AMINO ACID DIFFERENCE FORMULA TO HELP EXPLAIN PROTEIN EVOLUTION (1971), http://www.sciencemag.org/content/185/4154/862.long
You can find it in the original command "Grantham_score_calculator.py".
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