VMD-L Mailing List

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Mon Nov 26 2007 - 23:31:43 CST

hi John,
Thanks for the info. Just a quick question, how to calculate the SASA over
trajectoreis?

Thanks
Aneesh

On Nov 26, 2007 10:46 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>