My system is saving passwords in SHA-512 and DirectAdmin can't read them. I need MD5

Some newer OS's (Fedora 9) use SHA-512 by default. DA is often not compiled with support for SHA, so once a password is changed, DA calls the "passwd" program, which would set the new password into SHA-512.  DA would then not be able to use it, and you wouldn't be able to login.

CentOS / Fedora
The solution is to edit:

/etc/pam.d/system-auth-ac

Find the line:

password    sufficient    pam_unix.so sha512 shadow nullok try_first_pass use_authtok

change it to:

password    sufficient    pam_unix.so md5 shadow nullok try_first_pass use_authtok

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On Debian systems, edit:

/etc/login.defs

and change:

#MD5_CRYPT_ENAB  no

to

MD5_CRYPT_ENAB  yes

which tells the chpasswd command, called by DA, to use the MD5 instead of SHA-512.

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FreeBSD
Edit the /etc/login.conf, find the line

:passwd_format=sha512:

and replace it with:

:passwd_format=md5:

Then run the following to rebuild the /etc/login.conf.db from the /etc/login.conf file:

cap_mkdb /etc/login.conf