VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 12:03:43 CDT

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