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If your computer has two hard disks on the IDE controller and you are installing MINIX 3 to the second one, sometimes there can be a problem booting. This problem occurs if the second disk does not have a correct boot program in the MBR (Master Boot Record). To solve this problem, boot MINIX 3 from the CD-ROM, log in as root, and type:
installboot_nbsd -master /dev/c0d0 /usr/mdec/mbr
This command will install a proper MBR on drive 0 and you should not have any more problems.