VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 12:35:58 CDT

Joyce,
  The PSF file produced by the script generated some bonds to atoms with
index 0. PSF files use 1-based indexing, so this is the reason that VMD
won't load it. The crash you saw is already fixed in a later version of
the plugin, and only happened when reading bad PSF files.

Maybe someone has a newer or fixed version of the Gromacs top2psf.pl script
somewhere? Clearly it should not be generating bonds to atom index 0...
I would suggest asking on one of the Gromacs mailing lists, maybe the version
of the script I found in Google is old and has been replaced by a newer one?

Cheers,
  John

On Wed, Oct 20, 2010 at 01:05:28AM +0800, Joyce Tan wrote:
> Here you go, John.
>
> Thanks a lot.
>
> On Wed, Oct 20, 2010 at 1:03 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Most likely there's a bug in that script. I didn't write it, I just
> did a google search for "gromacs make psf file" to find it. If you send
> me the PSF file it created, I can have a look at it and see what is
> wrong
> with it. The segmentation fault shouldn't occur even with a badly
> formatted
> PSF file, so if you can send me that file, it would be helpful.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Oct 20, 2010 at 12:58:00AM +0800, Joyce Tan wrote:
> > John.
> >
> > Thanks for your quick reply.
> >
> > I've generated the psf with the script u provided. But I've a
> problem at
> > loading it into vmd.
> >
> > vmd > Info) Using plugin psf for structure file
> /home/birg/Desktop/zz.psf
> > ERROR) Error reading bond information.
> > Segmentation fault
> >
> > Why this happens?
> >
> > I'm currently using vmd 1.8.7 on Ubuntu 10.04 64 bit.
> >
> > On Wed, Oct 20, 2010 at 12:39 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >
> > I believe the Gromacs tools come with a "top2psf.pl" PERL script
> > that you might want to try out:
> > http://www.gromacs.org/@api/deki/files/90/=top2psf.pl
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Oct 20, 2010 at 12:04:36AM +0800, Joyce Tan wrote:
> > > ok. Thanks for your reply.
> > >
> > > Can u point me how can I build the psf?
> > >
> > > Thanks
> > >
> > > On Tue, Oct 19, 2010 at 11:45 PM, John Stone
> <johns_at_ks.uiuc.edu>
> > wrote:
> > >
> > > Hi,
> > > In abscence of a structure file that explicitly specifies
> bond
> > > information,
> > > VMD uses a distance-based bond determination heuristic.
> If you
> > are
> > > seeing
> > > a bond where there should not be one, or you are expecting
> to see
> > one
> > > but
> > > there isn't one, then you should try to create a PSF file
> or
> > another
> > > structure file type that explicitly specifies the bonds
> for your
> > > structure
> > > so that VMD doesn't have to guess.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Tue, Oct 19, 2010 at 11:36:43PM +0800, Joyce Tan wrote:
> > > > Hi.
> > > >
> > > > I have my 5000 frames .xtc and .gro loaded into vmd.
> > > >
> > > > And I was trying to convert one of the frames into
> pdb
> > through
> > > this:
> > > >
> > > > set A [atomselect top protein frame 4998]
> > > > $A writepdb xx.pdb
> > > >
> > > > When I load xx.pdb into the vmd, one atom from one
> residue
> > is
> > > connected to
> > > > another atom from another residue. This particular
> bonding
> > was not
> > > found
> > > > in the trajectory file. I really don't understand why
> is
> > this
> > > happening.
> > > > Can someone help?
> > > > Thanks.
> > > >
> > > > Regards,
> > > > Joyce
> > > --
> > > NIH Resource for Macromolecular Modeling and
> Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> > > Email: johns_at_ks.uiuc.edu Phone:
> 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax:
> 217-244-6078
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078