I fixed this issue, I am putting the solution I tried to find,

I created one JSP, and saw which trusted certificate store is being used. My 
JSP gave me the answer, I added the root certificate in the trusted keystore 
shown by my jsp,, and it started working:)


<%...@page 
import="java.net.*,java.io.*,com.sun.net.ssl.*,com.sun.net.ssl.internal.ssl.Provider,java.security.*,javax.net.ssl.*,java.util.*"%>
<%
 String ls_resp = null;




        try {

                        String surl = 
"https://www.samba.com/b2b/epayments/sc/SCConnectRequest.svl";;
                        String ls_psswd = "Ol2882666";
                        String ls_cert_path = 
"/App1/web/install/samba/certificate/GODigitalID.pfx";

                        BufferedReader lo_bufferedReader = null;
                        BufferedInputStream lo_bis       = null;
                        com.sun.net.ssl.SSLContext ctx   = null;
                        com.sun.net.ssl.KeyManagerFactory kmf = null;
                        KeyStore ks                      = null;
                        java.net.URL uRL                 = null;

                        uRL= new java.net.URL(null,new String(surl),new 
com.sun.net.ssl.internal.www.protocol.https.Handler());
                        ctx = com.sun.net.ssl.SSLContext.getInstance("SSL");
                        kmf = 
com.sun.net.ssl.KeyManagerFactory.getInstance("SunX509");
                        ks  = KeyStore.getInstance("PKCS12");
                
                        char[] lc_psswd = ls_psswd.toCharArray();
                        ks.load(new FileInputStream(ls_cert_path), lc_psswd);
                        kmf.init(ks, lc_psswd);
                        ctx.init(kmf.getKeyManagers(), null, null);
                        SSLSocketFactory sslSocketFactory = 
ctx.getSocketFactory();
                Enumeration aliases = ks.aliases();
                        while (aliases.hasMoreElements())
                        {
                                out.println(aliases.nextElement());
                        }
           out.println("here 1");

                        
com.sun.net.ssl.HttpsURLConnection.setDefaultSSLSocketFactory(sslSocketFactory);
                    com.sun.net.ssl.HttpsURLConnection httpsURLConnection = 
(com.sun.net.ssl.HttpsURLConnection)uRL.openConnection();
                    
httpsURLConnection.setHostnameVerifier(httpsURLConnection.getDefaultHostnameVerifier());
                    out.println(System.getProperty("javax.net.ssl.trustStore"));
                    System.setProperty("javax.net.ssl.trustStore", 
"/usr/java/jre/lib/security/cacerts");
                    System.setProperty("javax.net.ssl.trustStorePassword", 
"changeit");
                      out.println("here 2");
                    out.println(System.getProperty("javax.net.ssl.trustStore"));
                    httpsURLConnection.setDoOutput(true);
                    httpsURLConnection.setDoInput(true);
                    httpsURLConnection.setRequestMethod("POST");
                    httpsURLConnection.setRequestProperty("Content-Type", 
"application/x-www-form-urlencoded");
                    OutputStream lo_out = httpsURLConnection.getOutputStream();
                     out.println("here 3");
                    //lo_out.write(qstring, 0, qstring.length);
                    lo_out.flush();
                    int c;

                    lo_bis = new 
BufferedInputStream(httpsURLConnection.getInputStream());
                    StringBuffer lo_tmp = new StringBuffer();
                      out.println("here 4");
                        while((c = lo_bis.read())!= -1) {
                                lo_tmp.append((char)c);
                        }
                        lo_bis.close();
                        lo_out.close();
                        ls_resp = lo_tmp.toString();
                        out.println("ls_resp"+ls_resp);



                } catch(Exception e) {
                        
                        out.println(e.toString());

        }
%>


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