VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 29 2008 - 16:57:39 CDT

Hi,
  You could probably get such a file directly from APBS, but VMD doesn't
presently have a means of generating such a file.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 26, 2008 at 04:38:52PM +0200, Raluca Mihaela ANDREI wrote:
> Thanks again! I have another question: it is possibile to have
> a file with the coordinates and the electrostatic potential of
> every vertex of the molecular surface? Something like .wrl
> file but instead of colours I would like to have the
> potential.
> Thanks,
> Raluca
>
>
> On Wed, 24 Sep 2008 10:50:29 -0500
> John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >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 

-- 
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