VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:39:47 CDT

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