Ok, Elisa sent me the input files and I figured it out.
Elisa, this is why I asked you to copy and paste my
input file directly to your computer and use it.
It's hard to tell in emails, but you have a single space
in front of each of the following lines of your input file,
like so:
space
|
v
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
&end
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END
That is enough to confuse pmemd (at least old versions).
Here is the correct run_md.in file:
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,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END' /
DISANG=dist_chi.RST
DUMPAVE=restraint.log
LISTIN=POUT
LISTOUT=POUT
&end
Keep DNA fixed with weak restraints
0.05
RES 1 48
END
END
Like I said, old versions of pmemd are very finicky.
This *should* work now, but upgrading to
amber12 would make your life, and ours, easier =)
I hope this helps (fingers crossed).
--Niel
Also, Dave's comments about the ewald section still
apply
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Received on Thu Apr 12 2012 - 09:00:06 PDT
