The default size for something called the "stack" on Linux and Mac OS X is too small for AutoDock to run. You need to tell the system to remove this limit, and this depends on which shell you are using. You can find out what shell you are running by typing:

  echo $SHELL

in a terminal.

If you are using "csh" or "tcsh", you should put this command:

  limit stacksize unlimited

in your "~/.cshrc" or "~/.tschrc", whichever one you have.

If you are using "sh" or "bash" (the default shell on many Linuxes and now on the latest version of Mac OS X, 10.3, aka Panther), then put this command:

  ulimit -s unlimited

in your "~/.bashrc" or "~/.bash_profile". (Note: Some people running Mandrake 9.1 have reported ulimit -s 131072 works better than ulimit -s unlimited .)

Either way, remember you will need to source your ".cshrc" or ".bash_profile" before this will take effect. Type source .cshrc or source .bash_profile at the prompt in the terminal. Now try running AutoDock again, everything should work properly now. (For the curious, you can type limit (csh & tcsh) or ulimit -a (sh & bash) and you will see what the value of the stack size is.)