VMD-L Mailing List

From: Ahmet yıldırım (ahmedo047_at_gmail.com)
Date: Thu Nov 07 2013 - 03:11:40 CST

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>

> 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/
> 

-- 
Ahmet Yıldırım