VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 17 2014 - 10:14:35 CST

Are you having VMD load it as "parm" or "parm7" when you load it with
the file selector (see the "file type" chooser)?

Cheers,
  John

On Wed, Dec 17, 2014 at 03:46:39PM +0000, Hannes Loeffler wrote:
> The prmtop is still in ASCII. Sander and pmemd can be made to write
> out restart files in NetCDF format. Coordinate files created by leap
> are in ASCII too.
>
> On Wed, 17 Dec 2014 08:49:19 -0600
> John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > Beyond the questions others have already asked, I would also ask
> > whether this is an old-style prmtop, or if it is actually a NetCDF
> > formatted file, which is used by the latest versions of AMBER.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Dec 17, 2014 at 11:03:32AM +0100, Norman Geist wrote:
> > > Have you tried recreating that prmtop?
> > >
> > > Did you create that prmtop file on windows?
> > >
> > > Have you checked the encoding of the file?
> > >
> > >
> > >
> > > If you have created the file on linux, try unix2dos on your
> > > prmtop and see if this fixes the problem.
> > >
> > >
> > >
> > > Norman Geist.
> > >
> > >
> > >
> > > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > > Auftrag von alex lin
> > > Gesendet: Mittwoch, 17. Dezember 2014 00:38
> > > An: vmd-l_at_ks.uiuc.edu
> > > Betreff: vmd-l: VMD crashing when loading prmtop files
> > >
> > >
> > >
> > > Hi,
> > >
> > >
> > >
> > > I am currently running in to vmd crashing error while I try to
> > > load my prmtop files. I was using 1.9.1 vmd on windows 7 and I
> > > upgraded to 1.9.2 but still the error occurs with no description of
> > > the error.
> > >
> > >
> > >
> > > error message is " winvmd has stopped working" and only option
> > > is to close the program.
> > >
> > >
> > >
> > > I can load other prmtop files and pdb files fine but the ones
> > > that I am trying right now does not work.
> > >
> > >
> > >
> > > Lin
> > >
> > >
> > >
> > >
> > 

-- 
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/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/