From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Oct 20 2017 - 15:14:39 CDT

Hi Sara,

RIGHT! I've seen this before... Basically, the rst plugin in newer VMD versions is interpreting the file you gave it as velocity information, rather than coordinate information, which is leaving the coordinates unset. As an intermediate fix, delete the number after the number of atoms on the first line. This (for reasons that I'm sure will make more sense once I look at the source again), is enough for VMD to correctly recognize that the file contains only coordinates.

-Josh

On 10/20/2017 02:00 PM, Capponi, Sara wrote:

Hello Josh,

In the attachment you can find the .psf and the .rst files.

This is what comes up from the terminal with VMD 1.9.1 and VMD 1.9.2. As I wrote, VMD 1.9.2 reads the system but it doesn't display anything on the screen. From the Graphics window is seems that the protein is read by VMD, all the parts of the systems are in there. However, no cellbox is displayed.

Sara

VMD 1.9.1

Info) Analyzing structure ...
Info) Atoms: 99723
Info) Bonds: 99740
Info) Angles: 38099 Dihedrals: 8637 Impropers: 638 Cross-terms: 221
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 32378
Info) Waters: 32150
Info) Segments: 10
Info) Fragments: 32156 Protein: 1 Nucleic: 0
Title:

This file contains velocity info.
The Restartcrd has 99723 atoms.
This restartcrd file has box info.
Box Dimensions are 99.998001 99.987000 99.967003 90.000000 90.000000 90.000000
Info) Using plugin rst7 for coordinates from file /Users/scapponi/Sara/Project_UCSF/NompC/systemSetUp/ank3_23to26/ank3_setUp_Oct18/setUp/ank3_22to27.rst
Info) Finished with coordinate file /Users/scapponi/Sara/Project_UCSF/NompC/systemSetUp/ank3_23to26/ank3_setUp_Oct18/setUp/ank3_22to27.rst.

VMD 1.9.2

Info) Analyzing structure ...
Info) Atoms: 99723
Info) Bonds: 99740
Info) Angles: 38099 Dihedrals: 8637 Impropers: 638 Cross-terms: 221
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 32378
Info) Waters: 32150
Info) Segments: 10
Info) Fragments: 32156 Protein: 1 Nucleic: 0
rst7plugin) Title:

rst7plugin) This file contains velocity info.
rst7plugin) The Restartcrd has 99723 atoms.
Info) Using plugin rst7 for coordinates from file /Users/scapponi/Sara/Project_UCSF/NompC/systemSetUp/ank3_23to26/ank3_setUp_Oct18/setUp/ank3_22to27.rst
rst7plugin) Importing velocities from restart file.
Info) Finished with coordinate file /Users/scapponi/Sara/Project_UCSF/NompC/systemSetUp/ank3_23to26/ank3_setUp_Oct18/setUp/ank3_22to27.rst.

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov>
Sent: Friday, October 20, 2017 2:43:09 PM
To: Capponi, Sara; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: problems reading rst file as amber7 restart with VMD 1.9.3

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.

-Josh

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?

Thanks,

Sara

---------------------------------

Sara Capponi, PhD

Cardiovascular Research Institute

University of California in San Francisco, UCSF

555 Mission Bay Blvd S, R452M

San Francisco - CA 94143