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convert the server's certificate and key to pkcs format:pkcs12 format (please note that the ca.crt is the ca that signed the server certificate, so it is the server CA, not the client CA)
openssl pkcs12 -in server.crt -inkey server.key -export -out server.p12 -nodes -CAfile ca.crt
afterwards, you should be able to look at the pkcs12 keystore using: /usr/local/jdk1.6.0/bin/keytool -list -keystore server.p12 -storetype pkcs12
convert the pkcs12 keystore to jks keystore:
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