VMD-L Mailing List

From: Lai zaizhi (laizaizhi_at_gmail.com)
Date: Tue Jun 22 2010 - 12:22:16 CDT

On Tue, Jun 22, 2010 at 12:54 PM, Lai zaizhi <laizaizhi_at_gmail.com> 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
>

and I still don't get the psf file

>
> 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
>>
>
>