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I've been using QuteMol for generating 3D animated molecular images and I've encountered a problem; for some reason that's a complete mystery to me when I create a pdb file for etravirine (using MarvinSketch to create a sdf file and then using OpenBabel to convert the sdf to pdb and add implicit hydrogens) and load it I found the bromine atom was all by itself with no bond connecting the two and I would like a bond in the image. Any ideas? Thanks in advance.

The following image is the result I'm getting from QuteMol.

The result I'm getting from QuteMol

Josh Pinto
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1 Answers1

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I haven't used MarvinSketch in a while, but isn't it a 2D editor?

Generation of 3D coordinates from 2D files often means trouble. I tried that recently with a 2D BKChem drawing of a trypticene-based ligand for another answer and the result was useless.

I definitely recommend the use of Avogadro as a free 3D editor. Please have a look at their website or the article in Journal of Cheminformatics.

My typical workflow here is:

  1. switch off auto-adding of hydrogen
  2. draw the skeleton with the right multiplicity of bonds, but using carbon only
  3. change the "wrong" carbons to heteroatoms
  4. let the program add the hydogen atoms
  5. run a force-field optimization
  6. manually adjust some dihedral angles
  7. run the force-field optimization again
  8. (optional) align a bond with one of the principal axis
  9. save as CML or MOL

I put a MOL file of etravirine created that way on pastebin. Please give QuteMol a try at it.

I generated a PDB from the molfile mentioned above and ran it through QuteMol. The image below shows that the $\ce{C-Br}$ bond does exist in the PDB file.

QuteMol output

Admittedly, checking the PDB file for the respective CONNECT x y line would have been a (less flamboyant) proof too ;-)

Klaus-Dieter Warzecha
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  • MarvinSketch can do both 2D and 3D SDF files. If I had accidentally used a 2D image what would have happened if that the image I shared wouldn't have any 3 dimensionality at all, it'd all be in the same plane. So that's not the problem. I've created 3D SDF files for conversion to PDB using OpenBabel with MarvinSketch before, without a problem. Additionally I use QuteMol to create animated gif structures. Can avogadro do this? Animated GIF file is pretty important, other formats will not work for my purposes. – Josh Pinto Mar 24 '14 at 10:33
  • @BrentonHorne I wasn't aware that MarvinSketch could do that. Anyway, something apparently went wrong along the line: SDF/MOL file output broken, PDB conversion faulty, PDB reading by QuteMol erroneous... I didn't suggest to replace QuteMole with Avogadro - but using an input file generated differently will help to lacalize the problem. – Klaus-Dieter Warzecha Mar 24 '14 at 10:42
  • Ah, so you're saying I should use Avogadro to open the sdf and then use it to create a pdb? Because whenever I open my pdb file (generated with MarvinSketch & OpenBabel) in Avogadro it shows the bromine bond just the way I want it. I think it must be a bug in QuteMol. – Josh Pinto Mar 24 '14 at 11:05
  • @BrentonHorne Actually my suggestion was to first use the SDF/MOL file that I uploaded to pastebin for you to see if that works :D – Klaus-Dieter Warzecha Mar 24 '14 at 11:08