VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Wed May 13 2015 - 09:52:28 CDT

Hi,

Atom 1146 has residue id 10 and "1" is in column 14, however the first allowed position is 15. So change your matlab script so that residue id starts in column 15.

Maxim

> On May 13, 2015, at 9:04 AM, Jeeno Jose <josejeeno_at_gmail.com> 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 <josejeeno_at_gmail.com <mailto:josejeeno_at_gmail.com>> wrote:
> 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 <mailto: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 <mailto: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/ <http://www.ks.uiuc.edu/~johns/> Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ <http://www.ks.uiuc.edu/Research/vmd/>
>
>