Since it's a linux server i will personally recommend that you follow a cold clone process of the linux server.
What it means is that you download the "cold clone cd" of the VMWare converter. Shutdown the server, and reboot it using this CD. That way the cloning process goes well. There is also an option to perform a hot clone while the server is up and running but i have run into issues with hot cloning of linux servers in the past (not red hat but suse linux).
Hope this helps.
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