VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Sep 20 2008 - 02:19:15 CDT

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