VMD-L Mailing List

From: Stéphane Pezennec (stephane.pezennec_at_rennes.inra.fr)
Date: Fri Feb 11 2011 - 08:25:43 CST

Hello everybody,

I am wondering why does the orientation of the dipole moment of a
protein (relatively to the molecule) change upon a move of the molecule.

Specifically, I:

- loaded pdb:1aki;
- generated hydrogens and charges, using the 'autopsf' plugin;
- calculated and visualized the dipole moment ('dipole moment watcher'
  or console:'measure dipole -masscenter') of the whole molecule;
- loaded 1hel;
- aligned the backbones 1aki -> 1hel,

and observed that the orientation of the 1aki dipole moment (relatively
to the molecule) had dramatically changed. Is this expected? If not,
where am I wrong?

Many thanks in advance,

Stephane 

-- 
Dr Stéphane Pezennec
INRA
UMR1253 INRA-Agrocampus Ouest STLO
Rennes - France