VMD-L Mailing List

From: Anneta Tzampazi (toulka_at_gmail.com)
Date: Mon Sep 08 2008 - 05:22:40 CDT

Hello again and thank you for your immediate support. I am writing because I
have encountered a problem concerning the rotation of my protein. I want to
study the albumin adsorption onto a graphite surface and my Professor and I
came up with the following idea: we will calculate the hydrophobicity of the
surface of my molecule and select the part of this surface which is more
hydrophobic, which will probably be the right conformation for my protein
and will interact with the graphite surface. In order to do so, we thought
that rotating the molecule round each axis and estimating the Van der Waals
forces will provide me with the information I need. But I have not succeeded
yet in rotating the molecule with exactly the way I want it. I need the
molecule to rotate round its geometrical centre and I tried via VMD to do
this. So, I followed these steps:

1) set sel1 [atomselect top all] , to select the whole molecule
2) set gc [measure center $sel1] , to get the {x y z} of the geometrical
centre
3) set M1 [trans offset $gc] , to set both the offset and centering matrices
to the coordinates of my geometrical centre

After these, when I use the command $sel1 move $M1 my protein shows up
somewhere in the screen and its rotational behaviour is not the behaviour I
want. I could use all the help you can give. I need my molecule to rotate
round its geometrical centre and round each one of the three axes. Thank you
in advance once again.

Yours,
Anneta