VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 17 2008 - 21:53:13 CDT

Hi,
  I assume you could write a script to do this kind of calculation
so long as you have a reasonable way to define what the "interface"
is. You might also look at some of the web servers out there that
do things like this, though you'll be limited to whatever canned
analysis and file formats they've developed:
  http://www.bioinformatics.sussex.ac.uk/SHARP2/intro.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 17, 2008 at 08:56:20PM +1000, bo baker wrote:
> Hello:
>
> Can VMD calculate interface propensity for all the residues in the
> protein complex?
>
> I notice that there is a VMD script "metal_environment" ? Finds the
> propensity of residues near given ion.
>
> If VMD can't do such analysis, could any one recommand me a program
> for such anaylysis? Not the commercial softwares.
>
> Thank you for your advice.
>
> Bo 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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