Resolution:
The adapter can be configured to refer to external SSL certificates for its EMS Sessions using:
--> the RuntimecertificatesDirectory GV for the certificates folder.
--> specifying appropriate GVs for the Identity file and its password.

This option is available from SDK5.6 and so adadb6.0 and Designer5.6 also have to be used to configure such a project.
Following are the steps.
--> set the parameter "java.property.EnableExternalCertificatesFeature true" in designer.tra.
--> configure the adapter and the basic parameters for it sessions.
--> enable Use "SSL option?"
--> set the value of the parameter "Trusted Certificates Folder" as %%RuntimeCertificatesDirectory%%
--> set the value of the parameter "Identity" to the Identity file configured in the project.
--> In the Identity file configure global variables can be used to specify the parameters like "URL" and "Password"

Please find attached two screen shots and a sample project.