Dear Team,
Thank you very much for providing such a wonderful program to help make
research and studying easier.
I have been trying to get a Protein Data Bank (pdb) Files Format for an analog
compound that was designed on free Trial version of PerkinElmer's ChemDraw
Professional to use in a docking study. I tried using the OpenBabel computer
program --and the command line execution-- to convert the compound from its
custom ChemDraw cdx format to the AutoDock required pdb format, unfortunately,
I have only managed to get compounds that did not have all of the important
functional groups linked, and in some cases the compound was reduced to points
when viewed the new format with DiscoveryStudio. Furthermore, I noticed that
when I converted the compound from cdx to the sdf format, I got the compound in
the perfect configuration, but it also goes bad when I try to convert to the
pdb format.I have also checked some of the OpenBabel resources available online
and learnt how to generate a 3D conformer from command prompt. I tried to
check the compound this time on DiscoveryStudio and the several functional
groups looked awkwardly joined. I tried to dock this compound in AutoDock and I
got an 'Error parsing the following line in pdb:..' message from the python
shell. I attached a JPEG of what the compound should really look like (sdf
format), what I got when I tried to generate the pbd from cdx format using
command prompt and what I got when I tried converting cdx directly to pdb.
I would really appreciate if you could advise me on what things I could do to
solve this problem and get good, executable compounds for docking. I look
forward to hearing from you soon. Thank you.
Best regards,
Emmanuel.
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