[AMBER] Converted PSF file (prmtop > psf) failed to open in ChimeraX but did in old Chimera
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
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
Thank you! I have the pdb and everything works perfectly.
Alex ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, August 29, 2023 3:19 PM To: Alexander Hung Lee Alexander.Lee@uga.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] [AMBER] Converted PSF file (prmtop > psf) failed to open in ChimeraX but did in old Chimera
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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
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Elaine Meng