VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Feb 01 2006 - 09:05:37 CST

John,
 Just to let you know: the EDM plugin of vmd 1.8.4b10 reads correctly
the ptraj created density files!!

Thanks ane best wishes
vlad

John Stone wrote:

>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/
>>
>>
>
>
>
> 

-- 
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/