VMD-L Mailing List

From: Raluca Mihaela ANDREI (r.andrei_at_sns.it)
Date: Wed Sep 24 2008 - 10:46:54 CDT

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