AMBER Archive (2003)

Subject: conformational sampling

From: Robert G. Endres (endresrg_at_ornl.gov)
Date: Thu Jan 23 2003 - 08:17:57 CST

Dear AMBER users,

for locally enhanced conformational sampling, one can use the module
ADDLES and subsequently sander.LES which allows an ensamble of the system
to evolve independently and so can sample more conformations.

Since the "copies" seem to start out with the same coordinates, does
anyone know if and how one can choose different initial coordinates, like
different rotamers of an amino acid side chain? Or, can one specify and
automate a range - lets say of dihedral angles - to start out with?

Any suggestions are welcome! Thanks.

-Robert