Unfortunately you can't set arbitrary MQ connection factory properties from Glassfish. This is a restriction of the MQ resource adapter. MQ 4.4 will have a new feature to allow you to do this.
However, according to the MQ 4.3 administration guide (p162) you can also configure this particular property using a Java system property (i.e. -DimqSSLIsHostTrusted=true). In Glassfish you can configure this by setting <jvm-options> in domain.xml (or its admin console equivalent). Let us know if that works.
Nigel
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