With Amber9 I am applying the scripts of web Tutorial 1B (polyA-polyT) to
another case. While the tutorial run OK, and the new case also run OK up to
section 4, relaxing structure before MD, the MD itself, with command line:
$AMBERHOME/exe/sander -O -i eqaeqb_gb_md1_12Acut.in -o eqaeqb_gb_md1_12Acut.out
-c eqaeqb_gb_init_min.rst -p eqaeqb.prmtop -r eqaeqb_gb_md1_12Acut.rst -x
eqaeqb_gb_md1_12Acut.mdcrd
did not run, tail -f telling:
"Could not find cntrl namelist"
File "eqaeqb_gb_md1_12Acut.in" reads:
# eqaeqb MD Generalised Born, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 12.0
/
-------------
A google search did not clarify the problem. As a newcomer to MD I apologize
for posting trivial questions, if this is the case.
Thanks
francesco pietra
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Received on Wed Jul 11 2007 - 06:07:30 PDT
