I'm trying to run the tutorials for amber7 but cannot get the
dynamics to run for the DNA example with explicit solvents:
http://amber.ch.ic.ac.uk/tutorial/polyA-polyT_New/index.html
Specifically, I run
sander -O -i min_ntr.in \
-o min_ntr.out \
-c parm.inpcrd \
-p parm.prmtop \
-r min_ntr.restrt \
-ref parm.inpcrd
with "polyAT.inpcrd" and "polyAT.prmtop" from earlier steps substituted
in for "parm.inpcrd" and "parm.prmtop".
I get the error message:
namelist read: variable not in namelist
apparent state: unit 5 named md_ntr.in
last format: list io
lately reading sequential formatted external IO
Aborted
Is there a mismatch between the namelist and the variables in md_ntr.in?
How can I fix this so that I can continue with the tutorial?
Thank you,
Mark Hsieh
Received on Wed Apr 10 2002 - 13:31:50 PDT
