VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 27 2007 - 16:27:58 CST

Aneesh,
  You'll want to look at how a few of the other trajectory analysis
scripts for VMD are typically written, so that you can model your script
after the same general layout. There are some examples in the VMD script
library, and more extensive examples in the VMD and NAMD tutorials.
Generally speaking, you'll load trajectory frames (either all at once,
or using a script like the BigDCD script in the script library), and
updating atom selections etc on each new frame, you'll calculate your
SASA values and store the results for plotting, output, or subsequent
analysis routines. Let us know if you have specific questions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 27, 2007 at 11:01:43AM +0530, aneesh cna wrote:
> 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
> > 

-- 
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/      Fax: 217-244-6078