VMD-L Mailing List

From: ivana adamovic (iadamovic_at_gmail.com)
Date: Wed Jan 31 2007 - 09:26:19 CST

Dear John,

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):
======================================
  I've posted test builds of the CHARMM PBEQ map reader for most
of the supported VMD platforms for interested parties to test out:
  http://www.ks.uiuc.edu/Research/vmd/alpha/pbeq/

Follow the instructions in the README to try it out on your
locally installed VMD. (requires VMD 1.8.4 or VMD 1.8.5)
I posted both the plugins and a VMD saved state to exercise the plugin
using the 1kdx test structure that Wonpil sent me instructions on
generating. I used a "Surf" surface in the example as that ships with
VMD, but you can also color MSMS surfaces, VDW, or any other space filling
representation by potential if you like.

There's an ABPS example here for more info on how to use the potential
map to color various representations:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/

==========================

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.

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...
==========================================

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 ...

Thanks a lot for your time and help,

Ivana