VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 21 2010 - 16:56:08 CDT

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