VMD-L Mailing List

From: Lai zaizhi (laizaizhi_at_gmail.com)
Date: Mon Jun 21 2010 - 17:33:07 CDT

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