Musharraf, a US ally, wants another five-year term as president.
He has promised to step down as military leader if re-elected and on Tuesday, appointed Lieutenant General Ashfaq Kiani, a former spy chief, as the vice-chief of the army. Kiani will succeed Musharraf as and when he steps down from his army post.
But his opponents want Musharraf to resign his military position beforehand. They say that the election should not be by the current, outgoing parliament but by a new assembly formed after a general election.
Pakistani opposition members of parliament backed by hundreds of flag-waving supporters marched on parliament on Tuesday to resign.
Imran Khan, the cricketer-turned-politician and one of the leaders of the anti-Musharraf Alliance for the Restoration of Democracy, said: "This is the first step to discredit the election process."
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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The MPs and about 600 supporters, most of whom waved the flags of the Jamaat-e-Islami party, marched from a parliamentary apartment building in Islamabad to the national assembly.
They shouted slogans such as: "This is the end of your show - Go Musharraf, Go!" and "A friend of America is a traitor".
Musharraf is expected to win as his allies dominate the current national and federal parliaments that are conducting the vote - but opponents hope that the more than 80 planned resignations will erode its legitimacy.
Two candidates standing against Musharraf in the election meanwhile lodged appeals in the supreme court against his re-election, saying that the nomination papers he filed last week were invalid.
Wajihuddin Ahmad, former supreme court judge, urged the court to reject Musharraf's nomination papers and stop Saturday's vote.
Ashtar Ausaf Ali, his lawyer, said: "The petition asks that all Musharraf's nomination papers be rejected and that the presidential election should be stayed."
The COAS [chief of army staff] should be declared ineligible and until a decision on the petition, the election should be stayed," Ausaf Ali said, shortly before he filed the petition on behalf of Ahmad.
Ahmad is a former supreme court judge who resigned in 2000 rather than swear allegiance to Musharraf, an army general who seized power in a coup in 1999.
Makhdoom Amin Fahim, who is contesting the vote and represents the party led by Benazir Bhutto, a former prime minister, has also urged the court to halt the vote.