Amber certainly used to steal the 6th column of an ATOM record for an extra digit when handling > 99,999 atoms and ChimeraX accepts that treatment. Does Amber do something different now? What does the 100,000th ATOM record look like?

On May 6, 2024, at 6:51 AM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi!

I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore.

Alex Lee
PhD Student
Woods Research Group
Department of Biochemistry & Molecular Biology
Complex Carbohydrate Research Center
University of Georgia

315 Riverbend Rd.
Athens, GA 30602
Email: ahl63010@uga.edu
Mobile: (470) 641-3884
_______________________________________________
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu
To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/