VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 15 2004 - 15:40:21 CST

Patti,
  If you can write out your electrostatic potential values in one of
the supported volumetric map formats, you will be able to load them
into VMD, display 3-D textured volume slices, isosurfaces, and with
the pre-release versions of VMD 1.8.3 you can also texture arbitrary
molecular geometry by such data. The list of supported volumetric
grid file formats is posted here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/

If you haven't yet selected a file format, I'd recommend the
Data Explorerer "DX" format due to the ease with which one can write
to that format.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 15, 2004 at 03:28:15PM -0600, Patti Schaefer wrote:
> Hi,
>
> I am trying to find a way to map electrostatic potential results to
> atomic positions and create a graphical representation of the results.
>
> I have used CHARMM to calculate the electrostatic potential using the
> finite difference PB algorithm. The results give me the electrostatic
> potential at grid points whose dimensions I have specified. Does
> anyone know an easy way to map those results onto the atomic
> coordinates of my protein and then use VMD to color the protein
> accordingly? Is this possible with VMD?
>
> thanks!
> Patti
>
> 

-- 
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