From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 22 2010 - 11:27:49 CDT

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