VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 23 2005 - 10:56:05 CST

Hi,
  You'll need to make sure that you load a PSF file so that your
molecule has basic charge information. If you run APBS on a molecule
with no charges you'll get a bogus result. I believe the ABPS web site
has a Perl script you can run to create PQR files from most PDB structures.

  John

On Wed, Feb 23, 2005 at 11:44:47AM +0100, matteo.pennestri_at_virgilio.it wrote:
> I have some problem with APBS Plugin Version 1.0 to perform electrostatic
> calculations.
>
>
> I use VMD 1.8.3 on WindowsXP.
> On the APBS tool I set the position of the /TEMP (I cearteed a directory
> callede C:\Programs\University of Illinois\VMD\TEMP) directory and of the
> apbsrun.tcl file in the setting menu.
> When I run APBS the software told me "Molecule is uncharged. Proceed?"
>
> How can I perform electrostatic calculation to show it on surface?
> Tahnks a lot
>
> Matteo Pennestri
> University of Roma.
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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