VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 22 2010 - 13:58:14 CDT

Hi,
  You need to load a set of atom coordinates as well, that should
cure the problem.

Cheers,
  John

On Tue, Jun 22, 2010 at 12:54:56PM -0400, Lai zaizhi wrote:
> hi, John,
> I use TkConsole, and the feedback information are following:
> >mol new myfile.prmtop waitfor all
> 0
> >set sel [atomselect top all]
> atomselect0
> >$sel writepsf myfile.psf
> atomsel:frame -1 out of range for molecule 0
>
> Any suggestions are very welcome. thanks
>
> On Tue, Jun 22, 2010 at 12:27 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I think what you actually want to do is this:
> mol new myfile.prmtop waitfor all
> set sel [atomselect top all]
> $sel writepsf myfile.psf
>
> Let me know if you need further help with this.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jun 22, 2010 at 11:34:23AM -0400, Lai zaizhi wrote:
> > hi, John, thanks for your reply. Another question is how to save
> prmtop as
> > psf file, I tried
> >
> > mol new myfile.prmtop waitfor all
> > animate write psf myfile.psf waitfor all
> >
> > But it seems that it doesn't work:-(
> >
> > the system shows:
> > info> save trajectory: 0 frame specified; no coordinates written.
> > On Mon, Jun 21, 2010 at 8:14 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >
> > If you just need partial charges, that ought to be preserved
> > when writing out as PSF in VMD. Let us know if you need more
> help.
> >
> > Cheers,
> > John
> > On Mon, Jun 21, 2010 at 06:33:07PM -0400, Lai zaizhi wrote:
> > > hi, John, thanks! What I need from the PSF file is the point
> charge
> > > information.
> > >
> > > On Mon, Jun 21, 2010 at 5:56 PM, John Stone
> <johns_at_ks.uiuc.edu>
> > wrote:
> > >
> > > Hi,
> > > You probably can't use VMD to do the kind of conversion I
> expect
> > > you are looking for (100% transfer of all info from the
> prmtop
> > file...)
> > > While VMD will let you load the prmtop and save it as a
> PSF, this
> > would
> > > likely not give you what you need to begin simulating in
> NAMD.
> > You'll
> > > need to tell us more about what you intend to do with the
> PSF
> > file you
> > > create.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > > On Mon, Jun 21, 2010 at 05:41:37PM -0400, Lai zaizhi
> wrote:
> > > > On Mon, Jun 21, 2010 at 3:56 PM, Lai zaizhi
> > <laizaizhi_at_gmail.com>
> > > wrote:
> > > >
> > > > Hi,
> > > >
> > > > I have the amber topology file .prmtop and .pdb
> file, now
> > I want
> > > to
> > > > convert them to .psf file using vmd. What should I
> do? I
> > found
> > > some
> > > > archieves, yet they don't include more details, and
> I also
> > check
> > > the
> > > > manual of psfgen. It seems like psfgen has no
> command to
> > convert
> > > prmtop
> > > > to psf. Any suggestions will be very welcome!
> thanks!
> > > >
> > > > Good day!
> > > > zaizhi lai
> > >
> > > --
> > > 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/      Fax: 217-244-6078