VMD-L Mailing List

From: Joyce Tan (joyce.tankh_at_gmail.com)
Date: Tue Oct 19 2010 - 12:38:24 CDT

Alright. Thanks.

On Wed, Oct 20, 2010 at 1:35 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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.plscript
> 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 of the script I found in Google is old and has been replaced by a newer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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>