VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 19 2005 - 10:22:21 CDT

Alex,
  Can you email me (not the whole list) a gzipped sample of one of
these files?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 19, 2005 at 10:58:55AM +0200, Alexander Spaar wrote:
> Hi,
>
> some days ago I posted a similar message concerning the import of
> UHBD-grid files.
> I tried the *.grd and the *.grid option of vmd, as well with the binary
> as with
> the ascii-grids. However, the formats are somehow different. The *.grid
> format seems
> to be similar, it gives no error message, but still doesn't display the
> maps.
>
> Do you think it is difficult to write a script or a plugin for this file
> format?
> The header looks as follows:
>
> title (a72)
> scale, dum2, idum1, idum2, idum3, idum4, idum5 (2e12.6,5i7)
> im, jm, km, h, ox, oy, oz (3i7,4e12.6) (im, jm, km: grid dimensions; h:
> spacing; ox, oy, oz: grid origin)
> dum3, dum4, dum5, dum6 (4e12.6)
> dum7, dum8, idum6, idum7 (2e12.6,2i7)
>
> followed by the grid slices:
>
> l, jm, km (l=1,im)
> ...
>
> For example:
> POTENTIAL (kT/e)
> 1.00000e+00 0.00000e+00 -1 0 193 1 193
> 193 193 193 1.00000e+00-8.92430e+01-9.75055e+01-1.06581e+02
> 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
> 0.00000e+00 0.00000e+00 0 0
> 1 193 193
> -4.64098e-10 -5.09704e-10 -5.59465e-10 -6.13721e-10 -6.72837e-10
> -7.37199e-10
> -8.07223e-10 -8.83348e-10 -9.66042e-10 -1.05580e-09 -1.15316e-09
> -1.25866e-09
> -1.37291e-09 -1.49651e-09 -1.63014e-09 -1.77446e-09 -1.93021e-09
> -2.09814e-09
> ...
>
> Many thanks,
> Alex
>
>
>
> John Stone 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
> >
> >On Fri, Apr 15, 2005 at 06:09:09PM -0700, Mengjuei Hsieh wrote:
> >
> >
> >>Hi,
> >>
> >>I am wondering that Is there any future plan for VMD to include
> >>function that read-in AMBER pbsa electrostatic potential map ?
> >>
> >>Thanks,
> >>--
> >>Mengjuei Hsieh
> >>
> >>
> >
> >
> >
>
> --
> ---------------------------------------------------------
> Dr. Alexander Spaar
> Center for Bioinformatics
> Saarland University
> PO Box: 15 11 50
> D-66041 Saarbrücken
> Tel: +49-681-302-64168
> e-mail: a.spaar_at_mx.uni-saarland.de
> ---------------------------------------------------------
> 

-- 
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