VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 08 2013 - 14:47:25 CST

Hi,
  Yes, I have been out of town helping with a GPU workshop in San Diego
and have not had an opportunity to chase down the next step in your problem
yet. There's no need to send repeated emails. If I'm able to give you a
suggestion to work around your problem, I will let you know. From the looks
of it, you might be getting an error condition from the APBS run, but it's
hard to say for sure. If APBS is returning a non-zero error code, that may
be what is causing the problem. You could check this by running APBS
by hand in a shell and see if it returns a success error code or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 08, 2013 at 10:31:42PM +0200, Ahmet y?ld?r?m wrote:
> I have asked to VMD-list this problem for 3-4 days but I dont still get a
> answer to solve the problem.
>
>
>
> I tried "Mache.pqr" (There are links of that file at the end of web
> site)
> from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd.
> as I said before. I loaded to VMD it. Then I run APBS in VMD. After the
> calculations finish:
>
> In new window: Error message: Output file missing or unreadable.
>
> I tried manually loading the .dx file (Please
> see https://www.dropbox.com/s/lt2r2ecxsycj0ki/pot-PE0.dx).
>
> Later, I tried visualization of .dx file but the following commands do not
> work.
> Go to the "Draw style" tab of the Graphical Representations window and
> change Drawing Method to "Surf" and Coloring Method to "Volume".
>
> That is, I could not make any changes on the graph.
>
>
>
> What can the problem be? Why do the graph change? Is there any problem in
> .dx file generated by APBS?
>
>
>
> By the way, I am using VMD 1.9.1 on Ubuntu 12.1
>
> 2013/11/8 Gmail2 <ahmedo047_at_gmail.com>
>
> I tried "Mache.pqr"
> from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd.
> In new window: Error message: Output file missing or unreadable.
> I tried manually loading the .dx file (Please
> see https://www.dropbox.com/s/lt2r2ecxsycj0ki/pot-PE0.dx).
> 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".
> What can the problem be? Why do the graph change? Ys there any problem
> in .dx file generated by APBS?
>
> Thanks in advance
> Ahmet Yyldyrym
> 7 Kas 2013 tarihinde 15:33 saatinde, Ahmet yyldyrym
> <ahmedo047_at_gmail.com> thunlary yazdy:
>
> I tried "Mache.pqr" from
> http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd.
> In new window: Error message: Output file missing or unreadable.
> I tried manually loading the .dx file (Please see
> https://www.dropbox.com/s/lt2r2ecxsycj0ki/pot-PE0.dx).
> 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 yyldyrym <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>
>
> 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 Yyldyrym
>
> --
> Ahmet Yyldyrym
>
> --
> Ahmet Yyldyrym 

-- 
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/