From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 19 2005 - 16:11:51 CDT

Alexander,
  The grid file you sent me can be converted to a binary grid file
using a simple Fortran conversion program that's packaged with APBS,
and subsequently loaded into VMD by selecting the "Grid" file type
when you load it. The converter program you want to use is the
"uhbd_asc2bin" program listed on this page:
  http://agave.wustl.edu/apbs/doc/html/user-guide/x422.html

Now that I have an ascii file to test with, it should be possible
to write a plugin to read the ASCII form as well, though I think
in the interest of quick turnaround, you can solve your immediate
problem by using the file converter program that comes with APBS.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 19, 2005 at 05:51:52PM +0200, Alexander Spaar wrote:
> Hi John,
>
> this is an example grid file with 17*17*17 nodes, 4.0 A spacing.
>
> Thanks in advance,
> Alex
>
>
>
> John Stone wrote:
>
> >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
> >>---------------------------------------------------------
> >>
> >>
> >>
> >
> >
> >
>
> --
> ---------------------------------------------------------
> 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
> ---------------------------------------------------------
>

-- 
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