VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 06 2013 - 10:31:14 CST

Hi,
  Have you checked to see whether the APBS run generated the DX file
listed in your log below?:
  /home/phy/Desktop/work/apbs.65693/pot.dx

If the file wasn't created, then something went wrong with the APBS
run that needs to be corrected. Have you run APBS by hand at all on
this machine and verified that it runs correctly with example input
files from the APBS tutorials? The VMD APBS plugin will only work
correctly if APBS runs without trouble, so it's worth checking APBS
by running it manually at least once.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 06, 2013 at 03:05:09PM +0200, Ahmet y?ld?r?m wrote:
> Dear users,
>
> I have a problem about APBS in VMD. There isnt response of this error in
> VMD mailing list. A I am using Ubuntu 12.1 . There is executable apbs in
> path /usr/bin/.
>
> 1.) I installed VMD 1.9.1
> 2.) phy_at_phy:~/Desktop/work$ vmd
> 3.) File-->New molecule-->Fine
> name-->Browse-->/home/phy/Desktop/work/final.pqr
> OK and LOAD in the VMD Main window
> 4.)Extensions a** Analysis a** APBS electrostatics in the VMD Main window
> 5.) Edit a** Settings in the APBS Tool window
> Working Directory: "/usr/tmp"-->Browse-->/home/phy/Desktop/work/
> Apbs Location:/usr/bin/apbs
> OK
> 6.) "0" calculation from the "Individual PB calculations (ELEC):" window.
> 7.) Status: Ready
> "Run APBS" in the APBS Tool window.
> 8.) VMD console window:
> .....
> A Using "molecular" surface definition;harmonic average smoothing
> A Solvent probe radius: 1.400 A
> A Temperature: A 298.150 K
> A Potential to be written to pot.dx
> A Solving PDE (see io.mc* for details)...
> A Calculating energy (see io.mc* for details)...
> A Calculating forces...
> A Writing potential to pot-PE0.dx
> ----------------------------------------
> CLEANING UP AND SHUTTING DOWN...
> Destroying force arrays.
> No energy arrays to destroy.
> Destroying multigrid structures.
> Destroying 1 molecules
> Final memory usage: A 0.000 MB total, 668.698 MB high water
> Thanks for using APBS!
> apbsrun) Cannot access output file
> /home/phy/Desktop/work/apbs.65693/pot.dx
>
> 9.) In new window: Error message: Output file missing or unreadable.
>
> How can I fix this ERROR MESSAGE?
>
> Thanks in advance
>
> --
> Ahmet 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/