AMBER Archive (2002)

Subject: (no subject)

From: Mark Hsieh (hsieh_at_abmaxis.com)
Date: Wed Apr 10 2002 - 15:31:50 CDT

I'm trying to run the tutorials for amber7 but cannot get the
dynamics to run for the DNA example with explicit solvents:

http://www.amber.ucsf.edu/amber/tutorial/polyA-polyT/equilibration.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