From: Alexander Spaar (
Date: Tue Apr 19 2005 - 03:58:55 CDT


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

Do you think it is difficult to write a script or a plugin for this file
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
 -8.07223e-10 -8.83348e-10 -9.66042e-10 -1.05580e-09 -1.15316e-09
 -1.37291e-09 -1.49651e-09 -1.63014e-09 -1.77446e-09 -1.93021e-09

Many thanks,

John Stone wrote:

> 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.
> John Stone
>On Fri, Apr 15, 2005 at 06:09:09PM -0700, Mengjuei Hsieh wrote:
>>I am wondering that Is there any future plan for VMD to include
>>function that read-in AMBER pbsa electrostatic potential map ?
>>Mengjuei Hsieh

   Dr. Alexander Spaar
   Center for Bioinformatics
   Saarland University
   PO Box: 15 11 50
   D-66041 Saarbrücken
   Tel: +49-681-302-64168