VMD-L Mailing List

From: Jeeno Jose (josejeeno_at_gmail.com)
Date: Wed May 13 2015 - 03:12:52 CDT

I generated using MATLAB file operations.

 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:

    1142 9 ABC C2 C2 0.000000 12.0107 0
    1143 9 ABC C3 C3 0.000000 13.0186 0
    1144 9 ABC C7 C7 0.000000 15.0344 0
    1145 9 ABC C5 C5 0.000000 15.0344 0
    1146 10 ABC C6 C6 0.000000 15.0344 0
    1147 10 ABC C2 C2 0.000000 12.0107 0

Thank you

Jeeno Jose

On Wed, May 13, 2015 at 12:19 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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,
> John Stone
> 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) ' 1146
> > 10 ABC C6 C6 0.000000 15.0344 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>