VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Sun Oct 17 2010 - 18:52:00 CDT

Dear VMD users and developers:

I have 200 pdb structures taken each 50ps from an MD trajectory. I want to
eliminate the redundancy and find the non-overlaping set of structures that
represents the dynamics of my system. The problem is that when I try to
search for the non-redundant set using the srtucture QR(after aligning my
structures with STAMP) (with what ever QH cut-off) I dont get nothing,
actually it looks as if nothing happens at all. If I use the sequence QR
instead I get results but I will get one representative only.

Im I doing something wrong? Should I get a selection after the process? It
is enough to use the Qres tree from the pylogeneric tree menu??

Any help will be appreciated.

PS: I've done this same proces with VMD 1.87 in lunux and mac...

Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.