I have opened a PDB file in Avogadro in order to do QM calculations. However, when I open the file in Avogadro, certain bonding distances change compared to the input coordinates. It’s “only” about 0,05 Å, but it does make a difference in this case unfortunately. Why’s this, and can it be fixed?
Thank you in advance!
I don’t know of anything that would change interatomic distances at all.
Can you please give a bit more information?
- Version of Avogadro
- OS you’re using
- Example file (e.g., through Google Drive, Dropbox, etc.)
Thank you so much for the input! I realized the issue was not with Avogadro now, which was right all along! The issue was with the other program I opened the PDB in… Sorry for posting before looking at that possibility thoroughly! Thanks again! And thanks for a great program!