In a release posted on the school's Web site, university officials said Ammons submitted his letter of resignation to Chairman Solomon Badger III and members of the Board of Trustees.
The campus Ammons headed has been in turmoil since the hazing death in November of FAMU marching band drum major Robert Champion. In May, 11 people were charged with felony hazing in Champion's death and last month the Board of Trustees issued a vote of no-confidence in Ammons.
"After considerable thought, introspection and conversations with my family, I have decided to resign from my position as president in order to initiate my retirement on Oct. 11, 2012," Ammons said. "Following the presidency, I will continue my work on science, technology, engineering and math initiatives as a tenured full professor on our great faculty."
Ammons has been president since July 2, 2007.
"I am saddened by President Ammons' decision to resign, but it is his choice to do so," Badger said. "Given all that has transpired, it seems to be in the best interest of the university and I applaud him for putting FAMU ahead of his personal goals."
The Famuan, the school's student newspaper, reported the trustees would hold an "emergency call-in" meeting Monday morning.
"We must be able to provide the leadership necessary to discuss this grave issue," Trustee Narayan Persaud said.
"It is so important that we cannot wait," Trustee Rufus Montgomery said. "We all have a right to understand what that means given this time in our history."
The newspaper said reaction to Ammons' departure ranged varied.
"FAMU needs a clean sweep, maybe this was the start," criminal justice alumna Jamise Coyle said. "FAMU can only go up from here."
Alumna Miaisha Mitchell said she was "shocked" when she got the word.
"I feel like Ammons didn't get a chance to work with the university," she said. "He wasn't given an opportunity to correct the situation that was presented to him."
Champion, 26, was a member of FAMU's highly regarded "Marching 100" band when he collapsed and died Nov. 19 on a bus parked outside an Orlando hotel after a football game.
His parents, Robert and Pamela Champion, filed a wrongful-death lawsuit in February against the charter bus company and driver of the bus on which Champion was beaten. A family spokesman said this week they intend to file a lawsuit against the university, the Orlando Sentinel reported. They had to wait at least six months to take legal action against FAMU because it is a state institution, the Sentinel said.
The university released records last week indicating the dean of students had recommended three days before the Nov. 16 hazing incident that the band be suspended because of concerns about hazing, the Sentinel said.
Allegations of hazing against other band members have surfaced since Champion's death, and the university has been criticized for not doing more to prevent hazing.
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