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Hi Alex,
That link does not suggest simply changing the suffix.  It says how to convert prmtop to psf using the cpptraj program.  I don't know anything about ParmEd, but the error message from ChimeraX suggests the psf isn't quite right.  Instead of trying to use psf, do you have a PDB file of the atomic structure?

ChimeraX can use either a PSF file or a previously opened PDB file to define the connectivity of the atoms in the .nc trajectory.  It does not read prmtop files like Chimera does.

If you have a PDB file of the atomic structure, in ChimeraX you would open that first.  Then, you can open the .nc file as a trajectory using the "open" command with the "structureModel" option to specify the model number of the previously opened atomic structure.

This is explained in the "open" manual page, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>

Then you can play back the trajectory with the slider graphical interface, or with the "coordset" command (e.g. within a script).
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 29, 2023, at 11:13 AM, Alexander Hung Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> I converted prmtop to psf to use with ChimeraX by just editing the suffix as suggested http://archive.ambermd.org/201902/0118.html and also converted it a second way with ParmEd. ChimeraX couldn't read either version and gave me the error "list index is out of range." I successfully opened the original prmtop and the two psf versions in the old Chimera with trajectory .nc file. What do I need to do?
> Alex