VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 26 2007 - 11:16:08 CST

Aneesh,
  There's no built-in feature for doing such a calculation, but you could
perform a solvent accessible surface area calculation on an atom
selection on the hydrophobic structural components, and that should do
the job. Please read the VMD User's Guide to learn how to use the
'measure sasa' command, and then see some of the SASA scripts
previously posted on VMD-L for examples of how to do things like this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 26, 2007 at 03:39:44PM +0530, aneesh cna wrote:
> hi Alex,
> Thanks for reply. I want to compute "total hydrophobicity" of
> the protein just like calculating total solvent accessible surface
> area or in other words how much hydrophobic area of the protein is
> exposed. Hope this wil help you
>
> cheers
> Aneesh
>
> On Nov 26, 2007 12:19 AM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Sun, 25 Nov 2007, aneesh cna wrote:
> >
> > AC> hi Peter,
> > AC> Thank you for kind reply.Actually I want to calculate the surface
> > AC> hydrophobicity of a protein.
> >
> > aneesh,
> >
> > i don't think this is helping much.
> > could you please explain you mean by
> > "calculate the surface hydrophobicity"?
> >
> > i.e.:
> > do you want to visualize which part of
> > the surface is hydrophobic?
> > or:
> > do you want to get some parameter showing
> > what fraction of the surface is hydrophobic?
> > or:
> > do you want to compute some "total hydrophobicity"
> > of your protein? in this case, you'd have to
> > specify, how you want to measure it.
> >
> > can you give us an example, a program, or a paper
> > that does already what you want to do?
> >
> > cheers,
> > axel.
> >
> > AC>
> > AC> with regadrs
> > AC> Aneesh
> > AC>
> > AC>
> > AC> On Nov 24, 2007 8:06 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > AC> > Hi Aneesh,
> > AC> > if you could be more specific about what you mean by "a hydrophobicity
> > AC> > plot" we may be able to help; there are multiple definitions I can think
> > AC> > of for what you may be looking for.
> > AC> > Best,
> > AC> > Peter
> > AC> >
> > AC> >
> > AC> > aneesh cna wrote:
> > AC> > > hello vmd users,
> > AC> > > I would like to know whether there is any way to get a
> > AC> > > hydrophobicity plot for a protein (with more than 200) residues using
> > AC> > > VMD.
> > AC> > >
> > AC> > > with regards
> > AC> > > Aneesh
> > AC> > >
> > AC> >
> > AC>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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