Exporting multiple conformations in PDB format

General Discussion
1

Hi there,
I was googling around and found that there was, at one time, a script that allowed you to export the conformers generated in a conformer search in Avogadro. The scenario that is particularly useful is if you wanted to hold some parts of a molecule fixed and generate conformers for only certain parts. The link that was given was “http://avogadro.cc/wiki/Saveconformers.py”(ResearchGate)

Is this still around somewhere?

Thank you!

2

Yeah, I’m not sure where that reference came from… You’re not the first person to ask me that this month. :slight_smile:

I believe it’s from this work by Tim:

The problem is:

  • it required the Python support for Avogadro 1.x, which was rarely built
  • I don’t have the script … it was only uploaded to the wiki

My suggestion at the moment is to use Open Babel or RDKit to generate conformers, but it’s not easy to fix atoms as you describe.

It’ll be a few more weeks at least until I can get the new forcefield code finished for Avo2.

IIRC, if you save to XYZ, it will export all the conformers / coordinates, though.