VMD-L Mailing List

From: Finley Clark (fc36_at_rice.edu)
Date: Fri Jun 20 2025 - 13:41:29 CDT

Hello all,

I find that VMD (trying v. 1.9.3 and v2.0.0a5) can load CIF files
downloaded directly from the PDB, such as 1r69.cif, but cannot load CIF
files written by the OpenMM Python API's pdbxfile.PDBxFile.writeFile.

This happens even when I create the OpenMM CIF file by first loading the
PDB-sourced file into OpenMM, then writing it immediately without making
any changes to the topology or coordinates.

In VMD 1.9.3, the specific error message that I get is:
Info) File loading in progress, please wait.
pdbxplugin) Could not get atom number
Segmentation fault (core dumped)

And in 2.0.0.a5:
Info) File loading in progress, please wait.
pdbxplugin) Could not get atom number
pdbxplugin) error opening file.
ERROR) Could not read file 1r69_openmm.cif
ERROR) Loading of startup molecule files aborted.

In general, I'd like to be able to load systems that cannot be easily
represented in PDB format, so converting CIF files to PDB format before
loading in VMD is not a great workaround.

Any advice from the community would be appreciated!