VMD-L Mailing List

From: Nuno Ricardo Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Thu Nov 30 2006 - 15:11:28 CST

HI Jay

If you are a new user, then you must start from the beginning, by reading the manual.
I can give you the following tips:

1- vmd already as built in commands that allows you to select the hydrophobic residues
2- also has in the scripts libarary (web page) a c.o.m script
3- the process will be something like this:

    select hydrophobic residues
    determine the com of the side chain of those select residues
    select the pairs of residues which have a distance between their com < 4 angst.

Sorry if this is to crude, but VMD is a great analysis tool. But for that, you need to give a little of your time. Just start by the tutorials on the web page.
Nuno
  ----- Original Message -----
  From: gcmc jie
  To: vmd-l_at_ks.uiuc.edu
  Sent: Thursday, November 30, 2006 7:41 PM
  Subject: vmd-l: draw hydrophobic contact

  Hi all,

  I want to indicate the hydrophobic contacts at the interface between two domains. hydrophobic contact is defined when the center of mass of distance between two hydrophobic side chains is less than 4 Å. I would like to draw lines to show these hydrophobic contacts.

  Since I am new to use VMD, I google and search vmd-mail-list, I could not find similar script?
  anybody can give me hint. thanks in advance.

  Jay