VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 19 2005 - 21:16:05 CDT

Thanks,
  it's helpful to have as much information on this file format as
possible, I appreciate your description and I'll download the test
dataset when I'm back at the lab tomorrow.

  John Stone
  vmd_at_ks.uiuc.edu.

On Tue, Apr 19, 2005 at 04:05:49PM -0700, Mengjuei Hsieh wrote:
> Hi John,
>
> This is the format, first it comes with invariant commented headers,
> then the grid size, origin, grid number, then finally the potential
> value like this:
>
> # the following data is provided:
> # h, gox, goy, goz
> # xm, ym, zm
> # phi(1:xmymzm) in kcal/mol-e
> # mapping between (i,j,k) and phi index:
> # i + xm * ( j-1 + ym * ( k-1 ) )
> # obtaining coordinates: xg = gox + h*i;
> # yg = goy + h*j; zg = goz + h*k
> 0.500000000000000 8.48434360032879 3.50733980000000 5.25667429967121
> 63 85 79
> -0.685886647608785 -0.692272931164146 -0.698618767180744 [deleted]
>
> I also put an example data package in
> http://apple.sysbio.info/~mjhsieh/files/pbsa_potential.tbz, you can
> open the structure with parm7/rst7 VMD options.
>
> Thanks
> --
> Mengjuei
>
>
> On 4/18/05, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > If you can provide me with an example file, I could certainly
> > have a look and determine how difficult it would be to write a new
> > potential map reader plugin for this format.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu 

-- 
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