The last time Secretary of State Hillary Rodham Clinton was in Pakistan, she was asked why the United States persisted in killing innocent civilians with its secret program of drone strikes. And she speculated that officials in the Pakistani government knew the whereabouts of Osama bin Laden and other leaders of Al Qaeda. The mood was less charged this time, which may not have been surprising, given that Mrs. Clinton brought $500 million worth of American aid to fix Pakistan’s power grid and to help with water distribution. But the deep gulf of misunderstanding between Pakistan and the United States was still on vivid display on Monday, the second day of Mrs. Clinton’s visit to Islamabad, as she prodded Pakistanis to do more against Islamic militants and explained why the United States was reluctant to share nuclear technology with a country that has a history of proliferation. “It would be very helpful if we could get them,” Mrs. Clinton said of Al Qaeda and Osama bin Laden during an interview with Pakistani television journalists. “I believe they’re here in Pakistan. ”Mrs. Clinton offered guarded support for peace negotiations with the Haqqani network and other insurgent groups as a way to end the war in Afghanistan. But she cautioned Afghans and Pakistanis to enter such talks with open eyes. From Pakistan, she was scheduled to fly to Kabul for the international conference on Tuesday. When she was asked at a town hall meeting in Islamabad why the United States has not offered Pakistan a civilian nuclear deal like the one it has with India, she delivered a stern reminder that the father of Pakistan’s nuclear program, Dr. Abdul Qadeer Khan, sold nuclear secrets to Libya and North Korea.