From: Axel Kohlmeyer (
Date: Sun Nov 25 2007 - 12:49:29 CST

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.


i don't think this is helping much.
could you please explain you mean by
"calculate the surface hydrophobicity"?

do you want to visualize which part of
the surface is hydrophobic?
do you want to get some parameter showing
what fraction of the surface is hydrophobic?
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?


AC> with regadrs
AC> Aneesh
AC> On Nov 24, 2007 8:06 PM, Peter Freddolino <> 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> >

Axel Kohlmeyer
   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.