QSAR - Conversion of .mol file to .mm3 file

Dear Colleagues
What is the best way to convert the .mol file to .mm3 format (to be used in Tinker software).
When I used the Babel for conversion I found some error in terms of defining the atom types.
For example, for the molecule
 
                   __
           C---C==N
           |
          C
             \
              C---O
               ||
               O

I converted the .mol file into .mm2 using Babel. I got the following output.

                                   Atom type

3.18330 -21.46250 0.00000 2( 1)
3.83290 -21.08750 0.00000 4( 2)
3.17920 -22.21250 0.00000 2( 3)
3.82500 -22.58750 0.00000 3( 4)
4.48120 -20.70980 0.00000 10( 5)
4.54580 -22.39170 0.00000 7( 6)
3.82080 -23.33750 0.00000 7( 7)

Atom Type Definitions in MM3

1 CSP3 alkane
2 CSP2 alkene
3 CSP2 Carbonyl
6 O in OH
7 O in Carbonyl
4 CSP Alkyne
10 NSP

As one would expect the two caron atoms (atom 1 and 3) to be of the type 1 (CSP3 Alkane), the BABEL defines it as atom type 2 (CSP2 alkene).
Am I missing something in the above or is there any better way of converting the .mol file to .mm3 file.

I would appreciate your help. Thanks.

S Parthiban
Jubilant biosys
Received on 2002-12-17 - 05:39 GMT