VMD-L Mailing List
From: Ahmet yıldırım (ahmedo047_at_gmail.com)
Date: Thu Nov 07 2013 - 07:33:26 CST
I tried "Mache.pqr" from
In new window: Error message: Output file missing or unreadable.
I tried manually loading the .dx file (Please see
But the following commands do not work. That is, I could not make any
changes on the graph.
Go to the "Draw style" tab of the Graphical Representations window and
change Drawing Method to "Surf" and Coloring Method to "Volume".
2013/11/7 Ahmet yıldırım <ahmedo047_at_gmail.com>
> I checked the output file in the path given. The APBS run generated .dx
> file. It's not empty. There is not problem when I tried manually loading
> the .dx file.
> 2013/11/6 John Stone <johns_at_ks.uiuc.edu>
>> Have you checked to see whether the APBS run generated the DX file
>> listed in your log below?:
>> 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.
>> John Stone
>> 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
>> > 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):"
>> > 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
> Ahmet Yıldırım
-- Ahmet Yıldırım