Ligand preparation

[amor san juan <amor_sanjuan ( ( at ) ) yahoo.com>]

Dear AutoDocker's community:
 Can someone recommend any other softwares for ligand preparation (aside from
 chemskestch5, babel &/or ADT). I need your help.
 Using Chemsketch5 I draw the benzamidine(ben.mol) structure then, used Babel to
 add  explicit hydrogens & ben.mol2 conversion. The result is flawed ben.pdbq
 file as viwed below:
 REMARK  2 active torsions (identified by new id numbers):
 REMARK  status: ('A' for Active; 'I' for Inactive)
 REMARK       I      3-  7 between atoms:  C3   and  C7
 REMARK    1  A      7-  8 between atoms:  C7   and  N1
 REMARK    2  A      7- 10 between atoms:  C7   and  N2
 ROOT
 ATOM      1  A1  <1>     1      -4.129   2.188   0.000  0.00  0.00
 0.000   2
 ATOM      2  A2  <1>     1      -4.129   1.362   0.000  0.00  0.00
 0.000   2
 ATOM      3  A3  <1>     1      -3.417   0.954   0.000  0.00  0.00
 0.000   3
 ATOM      4  A4  <1>     1      -2.705   1.362   0.000  0.00  0.00
 0.000   2
 ATOM      5  A5  <1>     1      -2.705   2.188   0.000  0.00  0.00
 0.000   2
 ATOM      6  A6  <1>     1      -3.417   2.604   0.000  0.00  0.00
 0.000   2
 ATOM      7  C7  <1>     1      -3.417   0.129   0.000  0.00  0.00
 0.000   3
 ENDROOT
 BRANCH 7 8
 ATOM      8  N1  <1>     1      -4.132  -0.283   0.000  0.00  0.00
 0.000   2
 ATOM      9  H6  <1>     1      -5.107  -0.581   0.000  0.00  0.00
 0.000   1
 ENDBRANCH 7 8
 BRANCH 7 10                                                      ATOM     10
 N2  <1>     1      -2.703  -0.283   0.000  0.00  0.00     0.000   3
 ATOM     11  H7  <1>     1      -2.703  -1.303   0.000  0.00  0.00
 0.000   1
 ATOM     12  H8  <1>     1      -1.819   0.227   0.000  0.00  0.00
 0.000   1
 ENDBRANCH 7 10
 TDOF 3
  ------------------
 Diagramatically, the steps I did to prepare ligand is:
   ben.mol -----> ben.mol2 ---------> ben.pdbq
            babel            autotors3
 Alternatively, I used ADT yet, the same zeros in last columns appeared (no
 charge present).
 Amor