Subject: Ligand preparation

From: amor san juan <[email-masked]>
Date: Tue, 14 May 2002 15:08:40 +0800

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