VMD-L Mailing List

From: Keith Refson (kr_at_isise.rl.ac.uk)
Date: Tue Mar 22 2005 - 12:30:46 CST

Aha, I can immediately see that this is a completely different file format
from the one I have. For beginners, mine is formatted and begins:

COMMENT
(E12.5)
      1.00000 1.00000 1.00000 90.00000 90.00000 90.00000
       17 17 17
        1 0 17 0 17 0 17
     -1.80629
     -1.77782
     -1.54669
     -0.70950
      0.62344

Perhaps I was mistaken in thinking I was successful with this format
previously. Could a former version have supported xplor, which I can
also generate?

Otherwise, perhaps you could recommend a suitable text of binary format
I should use, since I have to write the converter anyway.

Keith Refson

Justin Gullingsrud wrote:
> Hi,
>
> Could you try again with VMD 1.8.3 and let us know if you get the same
> problem? Failing that, here is some information from the source code
> which may be helpful:
>
> /*
> * "unformatted" binary potential map, as used by Grasp and DelPhi
> *
> * Format (fortran):
> * character*20 uplbl
> * character*10 nxtlbl,character*60 toplbl
> * real*4 phi(n,n,n)
> * character*16 botlbl
> * real*4 scale,oldmid(3)
> *
> * Where n is the length in grid units of each edge of the grid.
> *
> * More information can be found at:
> * <http://honiglab.cpmc.columbia.edu/grasp/grasp_contents.html#A.2>
> * <http://trantor.bioc.columbia.edu/delphi/doc/file_format.html>
> */
>
> Cheers,
> Justin
>
>
> On Tue, 22 Mar 2005 15:57:02 +0000, Keith Refson <kr_at_isise.rl.ac.uk> wrote:
>
>>I'm attempting to write a utility to import some charge-density data into VMD.
>>The data is on a regular grid, and I'm attempting to convert it to .grd file
>>format. I had a working version with an earlier version of vmd, but with 1.8.2
>>I get a file format error reported on attempting to read it into vmd.
>>
>> Unable to open file with plugin of type grd
>> Improperly formatted file header: uplbl.
>>
>>Can someone help me out with some documentation of the format required
>>and hopefully an example .grd file I can use as a template?
>>
>>Thanks
>>
>>Keith Refson
>>--
>>Dr Keith Refson,
>>Building R3
>>Rutherford Appleton Laboratory
>>Chilton
>>Didcot kr AT isise
>>Oxfordshire OX11 0QX DOT nd DOT rl DOT ac DOT uk
>>
>
>
> 

-- 
Dr Keith Refson,
Building R3
Rutherford Appleton Laboratory
Chilton
Didcot                          kr AT isise		
Oxfordshire OX11 0QX            DOT nd DOT rl DOT ac DOT uk