From: Vermaas, Joshua (
Date: Fri Oct 20 2017 - 14:43:09 CDT

Hi Sara,

Could you attach the offending .rst file and maybe a .psf to make it easy to reproduce? Based it working in 1.9.1 and not 1.9.2, it probably has *something* to do with missing periodic box information, since I'd imagine parmEd won't output it, and there were changes between VMD 1.9.1 and 1.9.2 to add support for periodic box info. It would be also be useful if you had output from the terminal. For instance, this is what comes up from the terminal if I run it on my own machine:

psfplugin) Detected a Charmm PSF EXTEnded file
Info) Using plugin psf for structure file pb5c-cgo.psf
psfplugin) WARNING: no impropers defined in PSF file.
psfplugin) no cross-terms defined in PSF file.
Info) Analyzing structure ...
Info) Atoms: 45
Info) Bonds: 47
Info) Angles: 70 Dihedrals: 98 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
rst7plugin) Title: TITLE : Created by VMD with 45 atoms

rst7plugin) This file has no velocity info.
rst7plugin) The Restartcrd has 45 atoms.
rst7plugin) This restartcrd file has box info.
rst7plugin) Box Dimensions are 0.000000 0.000000 0.000000 90.000000 90.000000 90.000000
Info) Using plugin rst7 for coordinates from file test.rst7
Info) Finished with coordinate file test.rst7.

I see the molecule pop up, so the loading process works for some rst7 files, but clearly not all of them.


On 10/20/2017 01:00 PM, Capponi, Sara wrote:

Dear all,

I am experiencing problems in reading an .rst amber file with VMD 1.9.3 but not with VMD 1.9.1.

I used Parmed to create the .rst file from a .psf and .pdb file I can read correctly with VMD 1.9.3. However, when I open the .rst file with VMD 1.9.3, no image of the protein appears on the screen. The procedure I followed is this one:

- loading the .psf file

- loading the .rst file as amber7 restart on the same molecule

The protein is loaded, because in the Graphics window of VMD 1.9.3 I can find all the residues, segname, chains, etc. But the protein is not displayed on the screen.

While VMD 1.9.2 and VMD 1.9.3 don't work, I tried exactly the same procedure with VMD 1.9.1 and it works: I can see the protein.

Do you have any explanations on why the upgraded version of VMD do not display the protein with psf and rst file and an old version does it? How can I fix this problem?




Sara Capponi, PhD

Cardiovascular Research Institute

University of California in San Francisco, UCSF

555 Mission Bay Blvd S, R452M

San Francisco - CA 94143