Edit etc/instantjchem.conf
in the Instant JChem’s directory. Append the following line to the end of the file:
jdkhome=<JAVAHOME>
where <JAVAHOME> is the absolute path of the home directory of the new Java. E.g.:
jdkhome=/usr/java/jdk1.5.0_10
Any other lines that starts with jdkhome=
has to be taken into comment (by placing a # character on the beginning of the line).