Looks like you're missing some pak files eg. my startup looks like this
Code:
DOOM 1.1.1286 linux-x86 Nov 24 2004 17:56:04
Hostname: pc2.moon-blue.com
Alias: pc2
local IP: 192.168.0.3
------ Initializing File System ------
Loaded pk4 /usr/local/games/doom3/base/game00.pk4 with checksum 0x7dafc4d4
Loaded pk4 /usr/local/games/doom3/base/game01.pk4 with checksum 0x16cf3b8a
Loaded pk4 /usr/local/games/doom3/base/pak000.pk4 with checksum 0x28d208f1
Loaded pk4 /usr/local/games/doom3/base/pak001.pk4 with checksum 0x40244be0
Loaded pk4 /usr/local/games/doom3/base/pak002.pk4 with checksum 0xc51ecdcd
Loaded pk4 /usr/local/games/doom3/base/pak003.pk4 with checksum 0xcd79d028
Loaded pk4 /usr/local/games/doom3/base/pak004.pk4 with checksum 0x765e4f8b
Loaded pk4 /usr/local/games/doom3/base/pak005.pk4 with checksum 0x8ffc3621
Current search path:
/home/madluther/.doom3/base
/usr/local/games/doom3/base
/usr/local/games/doom3/base/pak005.pk4 (63 files)
/usr/local/games/doom3/base/pak004.pk4 (5137 files)
/usr/local/games/doom3/base/pak003.pk4 (4676 files)
/usr/local/games/doom3/base/pak002.pk4 (6120 files)
/usr/local/games/doom3/base/pak001.pk4 (8972 files)
/usr/local/games/doom3/base/pak000.pk4 (2698 files)
/usr/local/games/doom3/base/game01.pk4 (2 files)
/usr/local/games/doom3/base/game00.pk4 (2 files)
...
...
the missing files should be on the game CD's, just copy them over to the directory where the rest of the *.pk4 files are and all should be well.
HTH
Mad.