From: Raluca Mihaela ANDREI (r.andrei_at_sns.it)
Date: Fri Sep 26 2008 - 09:38:52 CDT

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