VMD-L Mailing List

From: Francesca Mocci (francy_at_mvcch3.unica.it)
Date: Tue Nov 11 2003 - 09:11:11 CST

Hello!

I have an xplor map file (produced with the program ptraj of the
amber7 package)
and I want to display it with vmd.1.8.1
I downloaded the readedm.txt file from
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readedm/readedm.txt
I changed its name in readedm.tcl
and I followed the suggestion for the usage written in the readedm file:

vmd > source readedm.tcl
vmd > mol load pdb my_structure.pdb
vmd > readedm my_edm.map

and the following error occurred:
mol volume: size of data does not match specified sizes

this is the output in the vmd console:

> EDM Reader, opening Light/2na_light.map
> rdparm generated grid density
> Grid dimensions: X: 60, Y: 60, Z: 60
> Grid elements: 216000
> Grid orientation: a: 30.000, b: 30.000, c: 30.000,
> alpha: 90.000, beta: 90.000, gamma: 90.000
> xOrigin, yOrigin, zOrigin: -14.5, -14.5, -14.5
> xVec: 30.0 0 0
> yVec: -1.53102359078e-10 30.0 0
> zVec: -1.53102359078e-10 -1.53102359079e-10 30.0
> ZYX
> # of grids in 1 slide: 3600
> # of grids in 1 line: 6
> # of lines in 1 slide: 600.0
> 215964
> 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
> mol volume: size of data does not match specified sizes

It is quite clear that my edm format is not ok for readedm,
and I tried to change it in several way but with no results..

Did anybody solved this problem for xplor map file
 obtained by means of the program ptraj?
If not, it can be usefull for me
to have a look at an xplor map file that is accepted by vmd
in order to convert mine.

Thanks for your attention,
Francesca