I would like to run Prime with user-defined charges on, for example, unnatural side chains and methylated protein backbone. How do I do this?

From Maestro, write out the input file and then add the following keyword:

USE_MAE_CHARGES yes

This will cause Maestro to use the charges from the .mae partial charge field.

If you are running Prime MM-GBSA, add '-cmae' to the command-line invocation.

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