VMD-L Mailing List

From: Hugo Gutiérrez de Teran (hugo.teran_at_usc.es)
Date: Tue May 25 2010 - 06:48:04 CDT

Hi,

I have a MD simulation (dcd file) created with NAMD, using options -wrap
on. The protein is a dimer, and the problem in the visualization and
analysis is that often one monoper croses the PBC cell and appears on
the other side, while the other monomer remains in the original cell.
I tryed to align the protein with "align" command in RMSD trajectory
tool, but only subunit A remains unchanged, while subunit B fluctuates
between one or other side of the cell. This way I can not analyze the
RMSD or the interactions between proteins.
Any ideas?

Hugo 

-- 
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN) 
Phone +34 981563100 ext 13873
e-mail:hugo.teran_at_usc.es       
http://webspersoais.usc.es/persoais/hugo.teran/