Ok, now it is working, I was missing the root cert.
I generated a script that did all the work:
JAVA_HOME=/usr/java/latest
export JAVA_HOME
PATH=$JAVA_HOME/bin:$PATH
export PATH
THE_NAME=www.dummy.org
export THE_NAME
rm /root/.keystore
rm /usr/share/tomcat5/.keystore
openssl pkcs8 -topk8 -nocrypt -in ${THE_NAME}_key.pem -inform PEM -out
${THE_NAME}_key.der -outform DER
openssl x509 -in rootCA_cer.pem -inform PEM -out rootCA_cer.der -outform DER
openssl x509 -in intermediateCA_cer.pem -inform PEM -out
intermediateCA_cer.der -outform DER
openssl x509 -in ${THE_NAME}_cer.pem -inform PEM -out ${THE_NAME}_cer.der
-outform DER
cat ${THE_NAME}_cer.der intermediateCA_cer.der rootCA_cer.der >
${THE_NAME}_all_cer.der
javac *.java
java ImportKey ${THE_NAME}_key.der ${THE_NAME}_all_cer.der
cp /root/keystore.ImportKey /root/.keystore
cp /root/.keystore /usr/share/tomcat5/.keystore
keytool -keypass changeit -storepass changeit -list
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