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 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!