AMBER Archive (2006)

Subject: AMBER: DNA tutorial xleap help

From: Amanda Jonsson (
Date: Wed Feb 08 2006 - 12:56:32 CST

I'm new to Amber8 (and Amber in general) and am trying the polyA-polyT DNA
tutorial. Everything is fine until I get to the xleap command:

addions model Na+ 0

When I edit model -- I can see the ions were added in a straight line along
the bottom, perpendicular to the DNA helix. This also messes up the next
solvation step. I'm not sure what I'm doing wrong.

I'm using:

OS: Red Hat Linux release 9 (Shrike)
Hardware: AMD Athlon(TM) XP 2200+

Compile/configure flags

Configured and compiled on a Athlon MP using pgf90 5.2-4
OS: Red Hat Linux release 9 (Shrike)

make clean
./configure -athlon pgf90
vi config.h {change -0* to -fast and tp athlon to athlonxp
make serial
cd ../test/
make test


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