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Atwal sent down three birdies against four bogeys.
Atwal, who last week finished tied eighth at the Colonial, was a 10th tee starter and had three birdies on the 12th, 15th and 17th and a bogey on 16th to turn in two-under.
But on the second stretch, he dropped bogeys on the first, fourth and fifth and ended over-par.
Rory McIlroy shared the lead with Chris Riley at six-under 66 at the Murifield course.
McIlroy hit beautifully to shoot 32 on the front nine despite missing three birdie putts inside eight feet. On his last eight holes, he converted half of his eight birdie putts on his way to a 66.