From: John Stone (
Date: Mon May 08 2023 - 00:12:26 CDT

  STRIDE expects PDB atom naming to be used.
If you've got a PDB corresponding to the simulation, I would recommend
loading that first, and then add the trajectory and other data from
the NetCDF into that molecule in VMD.
By loading the PDB first, you'll get the PDB atom names.
If you don't have a PDB, then you may need to reassign the atom names
using VMD atom selections, or using external tools.


On Fri, May 05, 2023 at 10:41:15AM +0000, Hoang, Oanh Tu wrote:
> Hello,
> I am trying to visualize my .nc file in cartoon representation, but it looks more like ribbon and I get this error
> File /tmp/fileZy8xQn has too many atoms in residue LBV 6
> Error reading PDB file /tmp/fileZy8xQn
> ERROR) Unable to find Stride output file: /tmp/fileg0vpFq
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
> I read that it could be due to the difference in atom names between amber and vmd, but I still quite don't understand how I could solve that problem. Does anyone know what I could do ?
> Best,
> Hoang

Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801