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How to resolve "Security Warning: Untrusted VPN Server Certificate!" warning on Linux systems when running the AnyConnect VPN client:

Solution:

# cd into hidden '.cisco' directory:
$ cd /opt/.cisco/certificates

# rename ca directory
$ sudo mv ca ca.orig

# link system certificate directory to ca
$ sudo ln -sf /etc/ssl/certs/ ca

# restart vpn service
$ sudo /etc/init.d/vpnagentd restart

Source: GT FAQ