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Article ID: 1507 - Last Modified:

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 the charges from the partial charge field in the Maestro file to be used.

If you are running Prime MM-GBSA, you can pass this setting (in quotes) on the command line with the -prime_opt option.

Related Articles:

#1364: How do I run an extended loop prediction from the command line?

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