VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 20 2006 - 14:27:39 CST

Vlad,
  I've made the X-PLOR EDM reader plugin in VMD much more permissive in
it's acceptance of files that don't strictly follow the behavior of
the original X-PLOR and the X-PLOR docs. It loads your file fine now,
and should work with other similar files generated by 'ptraj' and other
utilities in the AMBER suite that are based on the same/similar code.
If you're in a hurry to use this you can either get the new code from
CVS and compile it on your machine, or use the next test version of VMD
which I'll probably post in a few days.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 20, 2006 at 06:12:18PM +0100, Vlad Cojocaru wrote:
> Hi John,
> Attached you have a example file (wat.grid) and a reference.pdb file
> .... When I try to load the wat.grid file into vmd as an XPLOR density
> map (on top of the pdb reference) I get the error below. The file can be
> loaded in chimera as X-PLOR density file ....
>
> I think this file should comply with the X-PLOR density format (at least
> that's what's written in the amber manual).. but I dont really have
> expereince with these formats ...
>
> Best
> vlad
>
> vmd error message:
>
> edmplugin: failed reading cell data
> edmplugin: cell on line 9 cell 2, of 417 lines
> ERROR) Error reading volumetric data set 1
>
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/ 

-- 
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