5
$\begingroup$

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering atoms, manually including connect bonds or connect bonds, changing A atoms to Cs, NA atoms to N, small case lettering, .sdf, .pdb or .mol inputs. Nothing worked!!!.

When any of those alternative solutions were converted by OpenBabel to their corresponding .pdbqt, none of them interpret the double bonds of triazine (c1ncncn1) correctly. Furthermore, sometimes they introduced double bonds in other parts of the molecules, misplaced them or broke them.

I enclose two of my Triazine derivatives in the .sdf format.

136627870N3+2.2
  MOLSOFT 09022111472D

 29 30  0  0  0  0  0  0  0  0999 V2000
    0.0000   -0.0000   -0.0000 O   0  0  0
    1.2534    0.7910   -0.0000 C   0  0  0
   -1.3507    0.7910   -0.0000 C   0  0  0
    2.5067    0.0608   -0.0000 N   0  0  0
   -2.7014    0.0608   -0.0000 C   0  0  0
    2.4581   -1.3994   -0.0000 C   0  0  0
    3.7601    0.8518   -0.0000 C   0  0  0
    3.7114   -2.1295   -0.0000 N   0  0  0
    1.1073   -2.1295   -0.0000 N   0  0  0
    3.7114    2.4094   -0.0000 C   0  0  0
    3.6628   -3.5898   -0.0000 C   0  0  0
    1.0587   -3.5898   -0.0000 C   0  0  0
    2.4337    3.1639   -0.0000 C   0  0  0
    2.3120   -4.3199   -0.0000 N   0  0  0
    4.9161   -4.3199    0.0000 N   0  0  0
   -0.2920   -4.3199   -0.0000 N   0  0  0
    2.3851    4.7214   -0.0000 C   0  0  0
    4.8675   -5.7801    0.0000 C   0  0  3
    6.1695   -3.5289   -0.0000 C   0  0  0
   -1.6428   -3.5289   -0.0000 C   0  0  0
   -0.3407   -5.7801   -0.0000 C   0  0  0
    3.5167   -6.5102    0.0000 O   0  0  0
    6.1208   -6.5102    0.0000 C   0  0  0
    7.4229   -4.2590   -0.0000 C   0  0  0
   -1.6914   -1.9713   -0.0000 O   0  0  0
   -1.6914   -6.5102   -0.0000 C   0  0  0
    7.3742   -5.7314   -0.0000 C   0  0  0
   -3.0422   -5.7314   -0.0000 C   0  0  0
   -4.3929   -6.4616   -0.0000 C   0  0  0
  1  2  1
  1  3  1
  2  4  1
  3  5  1
  4  6  1
  4  7  1
  6  8  2
  6  9  1
  7 10  1
  8 11  1
  9 12  2
 10 13  1
 11 14  2
 11 15  1
 12 16  1
 12 14  1
 13 17  1
 15 19  1
 16 20  1
 16 21  1
 18 15  1
 18 22  1
 18 23  1
 19 24  1
 20 25  1
 21 26  1
 23 27  1
 24 27  1
 26 28  1
 28 29  1
M  END
> <molFormula>
C20H38N6O3

> <smiles>
CCCCN(CO)c1nc(nc(n1)N1CCCCC1O)N(CCCC)COCC

$$$$
135839733N3+1.3
  MOLSOFT 09022111472D

 25 27  0  0  0  0  0  0  0  0999 V2000
    0.0000   -0.0000    0.0000 O   0  0  0
    0.0250    1.4637    0.0000 C   0  0  3
   -1.2260    2.2018    0.0000 N   0  0  0
    1.2260    2.1768    0.0000 C   0  0  0
   -2.4771    1.4387   -0.0000 C   0  0  0
   -1.2761    3.7281   -0.0000 C   0  0  0
    1.2135    3.7782   -0.0000 C   0  0  0
   -3.8032    2.2269   -0.0000 N   0  0  0
   -2.4521   -0.0626   -0.0000 N   0  0  0
   -0.0500    4.5163   -0.0000 C   0  0  0
   -5.0542    1.4637   -0.0000 C   0  0  0
   -3.7031   -0.8257   -0.0000 C   0  0  0
   -5.0292   -0.0375   -0.0000 N   0  0  0
   -6.3803    2.2519   -0.0000 N   0  0  0
   -3.6781   -2.3269   -0.0000 N   0  0  0
   -6.4304    3.7782   -0.0000 C   0  0  0
   -7.7065    1.5388   -0.0000 C   0  0  0
   -2.3770   -3.0901   -0.0000 C   0  0  0
   -5.0042   -3.0400   -0.0000 C   0  0  0
   -7.7565    4.5663   -0.0000 C   0  0  0
   -9.0326    2.3269   -0.0000 C   0  0  0
   -1.0759   -2.3520   -0.0000 O   0  0  0
   -5.0542   -4.4787   -0.0000 C   0  0  0
   -9.0826    3.8532   -0.0000 C   0  0  0
   -3.7531   -5.2419   -0.0000 C   0  0  0
  2  1  1
  2  3  1
  2  4  1
  3  5  1
  3  6  1
  4  7  1
  5  8  2
  5  9  1
  6 10  1
  7 10  1
  8 11  1
  9 12  2
 11 13  2
 11 14  1
 12 15  1
 12 13  1
 14 16  1
 14 17  1
 15 18  1
 15 19  1
 16 20  1
 17 21  1
 18 22  1
 19 23  1
 20 24  1
 21 24  1
 23 25  1
M  END
> <molFormula>
C17H30N6O2

> <smiles>
CCCN(CO)c1nc(nc(n1)N1CCCCC1O)N1CCCCC1

$$$
$\endgroup$
3
  • $\begingroup$ I moved the comments here, along with the prior chatroom discussion, to a chatroom for this site: chat.stackexchange.com/transcript/message/59075397#59075397. The moved chat comments are a bit further up in the room (they are sorted chronologically while the comments from this post are all listed as when they were moved. $\endgroup$
    – Tyberius
    Sep 6 at 14:38
  • $\begingroup$ There is a dedicated Open Babel mailing list: sourceforge.net/projects/openbabel/lists/openbabel-discuss $\endgroup$ Sep 7 at 16:11
  • $\begingroup$ Thank you Geoff. I wil contact them. For AutoDockVina I use the PyRx package gui for Vina. It is easier to handle,it parallelises the work and also contains OpenBable. $\endgroup$
    – Julio Coll
    Sep 7 at 18:22

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