Reply – problem with sdf->pdb conversion
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problem with sdf->pdb conversion
— by Roni Gordon Roni Gordon
Hello,

I'm trying to extract PDB/CIF files from a multi-structure SDF file.  At
the moment, I'm just writing out one at a time (based on molecule #
using -f and -l command-line options).  I have confirmed that the
extract is correct by writing to an intermediate MOL file; however, the
PDB file that is produced is quite incorrect, with improper
connectivity, etc., and the corresponding CIF file is also incorrect.

Here's the MOL snippet:

Structure36
 OpenBabel05300818252D

 11 11  0  0  0  0  0  0  0  0999 V2000
    1.2091    5.5646    0.0000 O   0  0  0  0  0
    2.7394    6.4432    0.0000 C   0  0  0  0  0
    1.2091    4.1920    0.0000 C   0  0  0  0  0
    2.4182    3.4862    0.0000 C   0  0  0  0  0
    0.0000    3.4862    0.0000 C   0  0  0  0  0
    3.4957    4.1061    0.0000 C   0  0  0  0  0
    2.4182    2.0725    0.0000 C   0  0  0  0  0
    0.0000    2.0725    0.0000 C   0  0  0  0  0
    4.6695    3.4251    0.0000 O   0  0  0  0  0
    1.2091    1.3667    0.0000 C   0  0  0  0  0
    1.2091    0.0000    0.0000 Br  0  0  0  0  0
  1  2  1  0  0  0
  1  3  1  0  0  0
  3  4  2  0  0  0
  3  5  1  0  0  0
  4  6  1  0  0  0
  4  7  1  0  0  0
  5  8  2  0  0  0
  6  9  1  0  0  0
  7 10  2  0  0  0
  8 10  1  0  0  0
 10 11  1  0  0  0
M  END

What I am doing wrong? No matter what I do, I can't seem to get a vali
PDB using OpenBabel, either directly from the SDF or the MOL file
itself.  However, I know the MOL output is valid, as I've used other
tools that can successfully produce a PDB/CIF pair (e.g. PRODRG).

Thanks in advance for any help.

Roni



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