VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 24 2008 - 10:50:29 CDT

You could probably modify the code in the apbsrun plugin to achieve your
goals. Take a look at the apbsrun.tcl file in the apbsrun plugin directory
in your VMD installation to see what I mean.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 24, 2008 at 05:46:54PM +0200, Raluca Mihaela ANDREI wrote:
> Thanks a lot!!! "logfile" is a very good command! I managed to
> do a lot of things with it in an automatic way but I was not
> able to retrieve in the .off file the commands to interact
> with APBS (the only commands that I have are the ones that
> interact with VMD). It is possible to have them? I would like
> to calculate the electrostatic potential with APBS, map it on
> a surface and then render it with VRLM-2. By now all I can do
> from an .off file is to read files that APBS already created
> but I am not able to create them.
>
> thanks,
> Raluca
>
> On Sat, 20 Sep 2008 02:19:15 -0500
> John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Hi,
> > Yes, you can write a Tcl script that does all of this
> >automatically.
> >If you're not familiar with how to write Tcl scripts, you'll
> >want to
> >read the VMD user's guide to learn basic scripting, and then
> >I'd suggest
> >playing with the "logfile" command, and looking at the
> >contents of a
> >VMD saved state file, both of which are good ways to learn
> >how to
> >do this fairly rapidly.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Sep 18, 2008 at 02:33:00PM +0200, Raluca Mihaela
> >ANDREI wrote:
> >>Thanks a lot! I managed to visualize the electrostatic
> >>potential but I would like to do it in an automatic way,
> >>because I need to calculate the electrostatic potential and
> >>then save as .wrl file in order to import it into a 3D
> >>software. This must be done in every frame of an animation.
> >>Is
> >>it possible to do all these from the command line of
> >>Windows?
> >>Thanks,
> >>Raluca
> >>
> >>
> >>On Tue, 16 Sep 2008 11:01:18 -0500
> >> John Stone <johns_at_ks.uiuc.edu> wrote:
> >>>
> >>>Hi,
> >>> What working directory did you use? It turns out that
> >>>there are some
> >>>issues with APBS and filenames that contain spaces. The
> >>new
> >>>versions of
> >>>APBS have fixed these problems, and we are in the process
> >>of
> >>>updating the
> >>>APBS plugin for VMD similarly, but in the mean time you
> >>will
> >>>likely need
> >>>to make a working directory path that contains no spaces,
> >>>e.g. c:/apbsrun
> >>>
> >>>Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Tue, Sep 16, 2008 at 10:28:02AM +0200, Raluca Mihaela
> >>>ANDREI wrote:
> >>>>
> >>>>Hi,
> >>>>I would like to visualize in VMD the electrostatic
> >>potential
> >>>>of a protein. I am following this tutorial:
> >>>>http://apbs.sourceforge.net/doc/tutorial/#vmd-sect
> >>>>I am working in Windows, I downloaded apbs-1.0.0. I
> >>imported
> >>>>the pqr file into VMD (1.8.6), then in APBS tool I wrote
> >>the
> >>>>paths for Working Directory and APBS Location, I ran APBS
> >>>>and
> >>>>I receive the following message error: "APBSRun:output
> >>file
> >>>>missing or unreadable". In the folder for Working
> >>Directory
> >>>>a
> >>>>.pqr and an .in files are created.
> >>>>Can somebody tell me what am I doing wrong?
> >>>>
> >>>>thanks!
> >>>>Raluca
> >>>
> >>>--
> >>>NIH Resource for Macromolecular Modeling and Bioinformatics
> >>>Beckman Institute for Advanced Science and Technology
> >>>University of Illinois, 405 N. Mathews Ave, Urbana, IL
> >>61801
> >>>Email: johns_at_ks.uiuc.edu Phone:
> >>217-244-3349
> >>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078