AM1 vs PM3 Charges in CoMFA?



 Hello Netters,
 I just read Dr. Holders comments about AM1 vs PM3.
 What caught my interest the most was that part about PM3 charges being
 "unreliable".
 I would like to hear comments from those in the know as to which method of
 generating charges, AM1 vs PM3, contributes to better/more useful CoMFA
 models?
 We have been using PM3 to generate structures and charges for various
 steroidal estrogens that are used ultimately in CoMFA.  Compared to X-ray
 data, we found that PM3 gives slightly better geometry than AM1 for typical
 estrogens (Thomas E. Wiese and S. C. Brooks, "Molecular Modeling of Steroid
 Estrogens: Novel Conformations and Their Role in Biological Activity" in
 The Journal of Steroid Biochemistry and Molecular Biology, In Press).
 However, we found AM1 to give very poor geometry of nitro and amino
 substituted estrogen analogues when compared to PM3.  So, to be consistent,
 we used PM3 for all compounds in the data set and have generated useful
 CoMFA models.
 I would also like to know if some body out there has a comment about
 CoMFA's generated using geometry from PM3 and charges from AM1?
 Thanks,
 Tom
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 Tom Wiese
 Brooks Group
 Department of Biochemistry
 Wayne State University School of Medicine
 540 E. Canfield
 Detroit, MI
 48201
 Phone: (313) 577-5605
 FAX: (313) 577-2765
 email: tom %! at !% sgih.roc.wayne.edu
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