AMBER Archive (2002)

Subject: Nmode

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Thu Dec 19 2002 - 15:07:47 CST

Is it possible to do normal mode analysis (using
nmode) on a system with explicit solvent in it? My
system has about 150 amino acid residues and
6000 TIP3P water molecules. When I try to
run nmode on this system (after resizing all relevant
parameters), the program stops abruptly without
giving an error message (but it dumps a core).

Also, is anybody aware of a reference which describes
the method used by nmanal to project the cartesian
normal mode eigenvectors onto internal coordinates?

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