VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 08 2005 - 15:24:57 CST

Hi,
  Thanks for the information, we're figuring this out now. It's not clear
if the problem is solvate or psfgen, but we'll have it fixed shortly as
we've reproduced the problem here also.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 08, 2005 at 03:44:30PM +0100, amodzelewska_at_iimcb.gov.pl wrote:
> John,
> I don't see the Windows version on the link below. The problem concerns
> only this version. Solvate in VMD1.8.4a22 on Linux works correctly.
>
> Anna
>
>
> > Hi,
> > Can you try out VMD 1.8.4 beta 2 and let me know if solvate works
> > correctly for your structure?:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Mon, Nov 07, 2005 at 02:31:59PM +0100, Anna Modzelewska wrote:
> >> Hi,
> >> I wanted to put a protein in the water box with the VMD1.8.4a22 on
> >> Windows2000.
> >> I did it as usually by typing in the TkConsole: "solvate arsmd.psf
> >> arfotwist.pdb -t 10" and I got an error:
> >>
> >> "reading structure from psf file arsmd.psf
> >> reading coordinates from pdb file arfotwist.pdb
> >> reading structure from psf file
> >> e:/programy/vmd184/plugins/noarch/tcl/solvate1.2/wat.psf
> >> Error processing bonds
> >> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over."
> >>
> >> I tried the same with VMD1.8.3 and it worked.
> >> Anyone know what is wrong?
> >>
> >> Best Regards
> >> Anna
> >>
> >> ************************************************************************
> >> Anna Modzelewska, M.Sc. amodzelewska_at_iimcb.gov.pl
> >> International Institute of Molecular and Cell Biology
> >> http://www.iimcb.gov.pl/
> >> Trojdena 4, 02-109 Warsaw, Poland
> >> phone: +48 22 5970721 fax: +48 22 5970715
> >> ************************************************************************
> >>
> >
> > --
> > 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