VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 31 2007 - 13:37:30 CST

Ivana,

On Wed, Jan 31, 2007 at 10:26:19AM -0500, ivana adamovic wrote:
> I am trying to visualize CHARMM electrostatic potential map (result of
> the PBEQ calculations) using VMD, I have found one of your previous
> e-mails on the topic (below):

[...]

> and tried out both :
> 1. http://www.ks.uiuc.edu/Research/vmd/alpha/pbeq/ and
> 2. http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/
>
> 1. I have followed all steps you have described in the 1. but couldn't
> see the example. The problem with the first one is as follows:
> ~/Desktop/1kdx ivana$ vmd -e 1kdx.vmd
> -bash: vmd: command not found
> This is something basic and I am sorry to bother you, but I don't
> really know what next to do.

No problem.
In the case of the Mac and Windows versions of VMD, it is easier to run VMD
by starting it using the Mac desktop and clicking on the icon.
>From there, you can run these commands in your VMD text console,
to load the examples as if you had started them from the command line:
  cd /your/home/directory/Desktop/1kdx
  play 1kdx.vmd

> 2. I have also tried (with VMD 1.8.4 MacBookPro):
> http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/
> so first I loaded .psf and coordinate file, had graphic representation
> set to SURF and after that I have tried: Load state (potential
> calculated with PBEQ in CHARMM), but it couldn't do it; it complained
> about unrecognized command...

I would suggest upgrading to VMD 1.8.5 on your MacBookPro, as the newer
version corrects several bugs in the 1.8.4 version on that platform, and
it should also perform noticably better. Regarding the error message,
what error message did you see? This may simply be an issue of not
being in the right directory when you loaded the saved state, or
something along those lines, but it would be helpful to see the
actual error message you're getting.

> So in the nutshell I would like to visualize CHARMM electrostatic
> potential using VMD. I would really appreciate if you could help me
> out with that ...

Try my suggestions above and let me know if you need more help.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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