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
Thanks,
Amanda
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Received on Sun Feb 12 2006 - 06:10:05 PST
