How can i manually discover the database and AP server ?

My original agent is named by domain name,i want to name it by host name.So i remove it from grid control.But when i upload the agent again,only host and agent will show up in grid control.I try to manully add database,but encounter this exception:
oracle.sysman.emSDK.emd.comm.CommException: IOException in sending Request :: Connection timed out: connect
Can anyone tell me what's the problem?And how to resolve it?
Thanks!

while posting please specify os ,Problem seem to agent is not running on that box
emctl start agent, emctl upload and check targets.xml what are the targets monitored by agent

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