Home   Manual

Cannot load animation generated by ORCA

I believe this to be a bug with Avogadro,

Environment Information

Avogadro version: 1.2.0
Operating system and version: Windows 10

Expected Behavior

Animation of molecule

Actual Behavior

“Trajectory file C:/OrcaCalculations/DNA/ACA/trajectory.xyz disagress on the number of atoms in the present molecule”.

Steps to Reproduce

I am trying to use ORCA and Avogadro to animate the molecular dynamics of the base pairs of ACA in DNA. I generated an orca input from avogadro then ran the following input, https://pastebin.com/grRT8WZF. The calculation was stopped early but here is a small part of the trajectory.xyz file that was outputted, as the file is too large for pastebin, https://pastebin.com/MY1RXsb4. When i try to run the animation with the outputted trajectory file from orca the following error is presented “Trajectory file C:/OrcaCalculations/DNA/ACA/trajectory.xyz disagress on the number of atoms in the present molecule”. I double checked to see if the generated orca input from avogadro and my output had the same number of atoms and they do. I am also trying to animate the same avogadro file I used to export the molecule.

My guess, from similar cases with jobs that stop early, is that there’s a frame at the end without the full number of atoms => so you’ll get that error.

Here’s a way to double-check. The file you put up on pastebin has 197 atoms + 2 lines for the atom count and title. So each frame should have 199 lines.

Check the number of lines in the file - I’m not familiar with Windows, but if there’s a command-line tool or something that just gives you a line count (e.g., wc file.xyz on Linux or Mac). See if it’s an integer multiple of 199.