From: Lai zaizhi (laizaizhi_at_gmail.com)
Date: Tue Jun 22 2010 - 11:54:56 CDT

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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>