VMD-L Mailing List

From: alex lin (90alex.lin_at_gmail.com)
Date: Wed Dec 17 2014 - 17:31:31 CST

I tried unix2dos command to modify prmtop files but no success.
VMD gives error messave if I try to load in parm saying"unable to load
molecule" and in command it says ERROR) could not read file
I tried on the linux system that I made my prmtop files and it is working.

Thanks All,
Lin

On Wed, Dec 17, 2014 at 10:14 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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/
>
>