VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Jul 03 2010 - 09:14:11 CDT

Hi,
  I can't write much as I'm traveling, here's the source code for
measure sasa:
  http://www.ks.uiuc.edu/Research/vmd/doxygen/Measure_8C-source.html#l01058

This should answer your questions until I return.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 02, 2010 at 12:19:06AM +0200, henri mone wrote:
> Dear VMD users,
>
> I'm using the "sasa" command in VMD to calculate the hydrophobic and
> hydrophilic surface of my system.
> I'm using the commands sequence as reported in [1].
> I have following questions:
>
> 1. I found several different algorithms to calculate the SASA. Which
> SASA algorithm is implemented in VMD. Can someone point me to the
> corresponding paper.
>
> 2. Which exact definition of hydrophobic and hydrophilic does VMD use?
> Can someone point me to the corresponding paper/ description.
>
> 3. To select the hydrophilic atoms I use the command "set phil
> [atomselect top 'not hydrophobic']". Does the selection "not
> hydrophobic" really select only the hydrophilic atoms or are some
> additional atoms (e.g. neutral atoms) selected? If additional neutral
> atoms are selected, how can I restrict the selection to only the
> hydrophilic atoms?
>
> Thank you
> Hneri 

-- 
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