With a little bit of work you should be able to use MM5 output to drive the CLM3.
First familiarize yourself with the contents and format of the default atmospheric files (eg 1998-01.nc) included with other CLM datasets. Also familiarize yourself with the CLM code that reads and handles the data from these files. You may need to modify one or two things in order for the CLM to read and work with MM5 output.
Maybe another user has actually done what you are asking for. See if you get another response...
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