CCL: structure optimization in CoMFA?

Dear all,
 I attempt to use the molecular structure optimized using ab inito
 method in CoMFA analysis. However, I find the result is much poor than
 that using structure optimized using molecular mechanics (powell
 method). I don't know why.
 Any suggestions will be appreciated. Thank you for your consideration
 on this matter.
 Best wishes,
 (Mr.) Jinsong Zhao
 Ph.D. Candidate
 School of the Environment
 Nanjing University
 No.22 Hankou Road, Najing 210093
 P.R. China
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