Using RAMD for studiying conformational changes in proteins

From: Raul Araya (
Date: Thu Mar 24 2011 - 15:23:39 CDT

Dear NAMD users and developers:

I'm interested on studying gating phenomena in protein channels. An I
became interested in AMD.
I have seen the RAMD library and the examples therein contained in the
CVS version of NAMD (an also avaliable in the 2.7 version), but they
seem to be limited mostly to be used in ligand/protein interaction
studies. Can it be used for example to induce or observe
conformational changes in proteins?
Being that the case, the "ligand" to be defined should correspond to a
domain, or part of the protein in study??

Any help will be appreciated

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.

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