Re: CCL:Ligand preparation



The file you produced this way is a 2D drawing. Therefore addition of
 hydrogens and any further manipulations are nonsense. You should use a real
 modelling application.
 Tamas
 ----- Original Message -----
 From: "amor san juan" <amor_sanjuan[ AT ]yahoo.com>
 To: <chemistry[ AT ]ccl.net>
 Sent: Tuesday, May 14, 2002 9:08 AM
 Subject: CCL:Ligand preparation
 > 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
 >
 >
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