From: [email-masked] (Xavier Fradera)
Date: Mon, 7 Jun 1999 14:29:54 -0200

Hi,

a few days ago, I asked for a program that could convert sybyl atom types to MM2 or other force-
fields for use in tinker. A. Stevens and C. Gonzalez suggested using the Babel program.

I have tried babel-1.6. It can read sybyl mol2 fields and write MM2, MM3 and tinker input files,
among other. However, I am not absolutely sure that the atom type conversion is done adequately.
For instance, I have tried translating a mol2 file for a small molecule (benz.mol2) to a tinker
file (benz.xyz) (files are at the end) The atom types generated for a tinker output coincide with 
those generated for MM2 and MM3, so i tried running tinker single-point energy calculations using 
the MM2, MM3 and tinker parameter sets. In all cases, tinker fails to calculate the energy because 
it finds bonds (and torsions) for which it has no parameters, e.g., for the MM2 force-field:

 Undefined Bond Stretching Parameters :

 Type             Atom Names           Atom Classes

 Bond            1-C       7-C+            2   30
 Bond            7-C+      8-N            30    9
 Bond            7-C+      9-N            30    9
 Bond            8-N      15-H             9   23

 etc. 

It happens the same for most of the molecules I have tried. Anyone has had similar problems ? Is 
this actually a problem in the atom type translation or rather a limitation of the MM2 force-field ?
(this molecule is actually [(C6H6)-C-(NH2)2]+)

Thanks.

--
Xavier Fradera

------------ (benz.mol2)

@<TRIPOS>MOLECULE
bezamidine
   18    18     1     0     1
PROTEIN
GASTEIGER
INVALID_CHARGES

@<TRIPOS>DICT
PROTEIN protein
@<TRIPOS>ATOM
      1 C1          6.2540   17.3460   23.1660 C.ar      1 BENZ1       0.0932
      2 C2          5.9180   16.1210   22.5890 C.ar      1 BENZ1      -0.0269
      3 C3          4.7620   16.0230   21.7990 C.ar      1 BENZ1      -0.0523
      4 C4          3.9480   17.1560   21.6060 C.ar      1 BENZ1      -0.0554
      5 C5          4.3030   18.3840   22.1750 C.ar      1 BENZ1      -0.0523
      6 C6          5.4510   18.4930   22.9710 C.ar      1 BENZ1      -0.0269
      7 C7          7.4670   17.4620   23.9910 C.cat     1 BENZ1       0.2620
      8 N8          8.2990   16.3920   24.2200 N.pl3     1 BENZ1      -0.2466
      9 N9          7.8230   18.6310   24.5880 N.pl3     1 BENZ1      -0.2466
     10 H10         6.5450   15.2514   22.7496 H         1 BENZ1       0.0693
     11 H11         4.4965   15.0781   21.3388 H         1 BENZ1       0.0653
     12 H12         3.0431   17.0764   21.0145 H         1 BENZ1       0.0649
     13 H13         3.6855   19.2573   21.9988 H         1 BENZ1       0.0653
     14 H14         5.7182   19.4387   23.4285 H         1 BENZ1       0.0693
     15 H15         9.1401   16.5092   24.8028 H         1 BENZ1       0.2545
     16 H16         8.0813   15.4731   23.8088 H         1 BENZ1       0.2545
     17 H17         7.2438   19.4728   24.4583 H         1 BENZ1       0.2545
     18 H18         8.6718   18.6745   25.1698 H         1 BENZ1       0.2545
@<TRIPOS>BOND
     1    1    2 ar
     2    1    6 ar
     3    1    7 1
     4    2    3 ar
     5    2   10 1
     6    3    4 ar
     7    3   11 1
     8    4    5 ar
     9    4   12 1
    10    6    5 ar
    11    5   13 1
    12    6   14 1
    13    7    8 1
    14    7    9 1
    15    8   15 1
    16    8   16 1
    17    9   17 1
    18    9   18 1
@<TRIPOS>SUBSTRUCTURE
     1 BENZ1       9 RESIDUE           1 I     ****    0 ROOT
@<TRIPOS>SET
UNK_ATOMS       STATIC     ATOMS    AMSOM    **** Atom types guessed for these atoms
9 1 2 3 4 5 6 7 8 9

------------ (benz.xyz)

    18 bezamidine
     1  C      6.254000   17.346000   23.166000     2     2     6     7
     2  C      5.918000   16.121000   22.589000     2     1     3    10
     3  C      4.762000   16.023000   21.799000     2     2     4    11
     4  C      3.948000   17.156000   21.606000     2     3     5    12
     5  C      4.303000   18.384000   22.175000     2     4     6    13
     6  C      5.451000   18.493000   22.971000     2     1     5    14
     7  C      7.467000   17.462000   23.991000    30     1     8     9
     8  N      8.299000   16.392000   24.220000     9     7    15    16
     9  N      7.823000   18.631000   24.588000     9     7    17    18
    10  H      6.545000   15.251400   22.749600     5     2
    11  H      4.496500   15.078100   21.338800     5     3
    12  H      3.043100   17.076400   21.014500     5     4
    13  H      3.685500   19.257300   21.998800     5     5
    14  H      5.718200   19.438700   23.428500     5     6
    15  H      9.140100   16.509200   24.802800    23     8
    16  H      8.081300   15.473100   23.808800    23     8
    17  H      7.243800   19.472800   24.458300    23     9
    18  H      8.671800   18.674500   25.169800    23     9