VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 13 2015 - 09:26:46 CDT

Hi,
  The PSF reader in VMD 1.9.1 was more permissive with misformatted files
than VMD 1.9.2 is, because the PSF parser in VMD 1.9.2 now supports new
PSF file features such as CHARMM cgenff parameters. This required tightening
up the PSF parsing, and most likely what's happening is that your PSF
file violates some column limits that were previously acceptable and now
are not. The fact that you're generating the file via Matlab scripting
also leads me to believe that it probably is caused by an imperfect
script for writing the PSF format.

Cheers,
  John

On Wed, May 13, 2015 at 07:34:07PM +0530, Jeeno Jose wrote:
> The PSF file not taken in 1.9.2, has been accepted in 1.9.1 !!!
> On Wed, May 13, 2015 at 1:42 PM, Jeeno Jose <[1]josejeeno_at_gmail.com>
> wrote:
>
> I generated using MATLAB file operations.
>
> Â Formatting may not be the issue since the entries for atoms preceding,
> say 1143, has the same size as that of 1145. Here is the relevant
> portion from the PSF:
>
> Â
>
> Â Â Â 1142Â Â Â Â Â 9Â Â Â ABCÂ C2Â Â C2Â Â Â Â
> 0.000000Â Â Â Â Â Â 12.0107Â Â Â Â Â Â Â Â Â Â 0
> Â Â Â 1143Â Â Â Â Â 9Â Â Â ABCÂ C3Â Â C3Â Â Â Â
> 0.000000Â Â Â Â Â Â 13.0186Â Â Â Â Â Â Â Â Â Â 0
> Â Â Â 1144Â Â Â Â Â 9Â Â Â ABCÂ C7Â Â C7Â Â Â Â
> 0.000000Â Â Â Â Â Â 15.0344Â Â Â Â Â Â Â Â Â Â 0
> Â Â Â 1145Â Â Â Â Â 9Â Â Â ABCÂ C5Â Â C5Â Â Â Â
> 0.000000Â Â Â Â Â Â 15.0344Â Â Â Â Â Â Â Â Â Â 0
> Â Â Â 1146Â Â Â Â 10Â Â Â ABCÂ C6Â Â C6Â Â Â Â
> 0.000000Â Â Â Â Â Â 15.0344Â Â Â Â Â Â Â Â Â Â 0
> Â Â Â 1147Â Â Â Â 10Â Â Â ABCÂ C2Â Â C2Â Â Â Â
> 0.000000Â Â Â Â Â Â 12.0107Â Â Â Â Â Â Â Â Â Â 0
>
> Â
>
> Thank you
>
> Jeeno Jose
>
> On Wed, May 13, 2015 at 12:19 PM, John Stone <[2]johns_at_ks.uiuc.edu>
> wrote:
>
> Hi,
> Â The number of atoms is not likely to be a problem, more likely
> there
> is some kind of formatting issue with your PSF file. How did you
> generate it?
>
> Cheers,
> Â John Stone
> Â [3]vmd_at_ks.uiuc.edu
> On Wed, May 13, 2015 at 12:08:25PM +0530, Jeeno Jose wrote:
> > Dear all
> >
> > While I was loading my PSF file which contains 1200 atoms, I got the
> > following messages:
> >
> >
> >
> >
> >
> >
> >
> >
> > *psfplugin) Failed to parse segname in PSF file:psfplugin)Â Â 'Â
> Â 1146
> > 10Â Â ABCÂ C6Â Â C6Â Â Â 0.000000Â Â Â Â 15.0344Â
> Â 0'couldn't read atom
> > 1145ERROR) molecule_structure: Unable to read structure for molecule
> > 1ERROR) molecule_structure: severe error indicated by plugin
> aborting
> > loading ofmolecule 1*
> >
> > Whereas, when I tried to load a smaller domain which contains only
> 960
> > atoms (everything same w.r.t to the domain of 1200 atoms, just
> differs in
> > total number of atoms), it loaded. Is there any limit of 1144 atoms
> in VMD?
> > I used to do load 1200 atoms in my previous installations of VMD
> 1.9.2.
> >
> > Is there any setting which I should change to resolve this?
> >
> > Thank you
> > Jeeno Jose
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [4]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [5]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:josejeeno_at_gmail.com
> 2. mailto:johns_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. http://www.ks.uiuc.edu/~johns/
> 5. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/