Hello,
There are still a number of issues with your input file (for example, a
non-existent namelist is terminated, you moved the &ewald namelist to
the bottom, but it's not terminated, and DUMPFREQ is _still_ not in
quotes)
This is a complex combination of input parameters. My suggestion is to
start with something easier -- the Amber manual, the tutorials, and the
test cases in $AMBERHOME/test are good starting points. This way, you
can experiment with more complex options one at a time (keep adding
something new to the input file to make sure you know what is
happening). Speaking from experience, you learn much more through trial
and error (with the aid of the tutorials and manual) than you do from
someone providing an answer each step of the way.
This should help give you a better understanding of Amber inputs which
will allow you to diagnose this issues quickly on your own in the
future.
Good luck,
Jason
P.S. For reference, I believe this is the 'correct' input file
('correct' in that I think it will now run):
run: MD
&cntrl
imin = 0, irest = 0 , ntx = 1,
nstlim = 2500000, dt = 0.002,
ntc = 2 , ntf = 2,
ntt = 3, gamma_ln = 2.0,
tempi = 298.0, temp0 =298.0,
ntb = 1 ,
ntpr = 250 , ntwx = 250, ntwr = 500 ,
cut = 9,
ig = -1
ioutfm = 1
nmropt=1,
ntr=1
/
&ewald
nfft1 = 90,
nfft2 = 90,
nfft3 = 90,
/
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END
&wt type='DUMPFREQ', istep1=1, /
&wt type='END' /
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Apr 01 2012 - 12:00:03 PDT
