Hello,
On Thu, 2012-03-29 at 15:04 +0200, Elisa Frezza wrote:
> Dear all
>
> I use amber 9 and I would like to use pmemd.
> I'll report my input file and I hope that someone may help me.
> The error is :
>
>
> rfree: Error decoding variable 1 3 from:
> DUMPAVE=restraint.log
rfree is the subroutine that parses the group-style input (stands for
free-format input). This suggests that pmemd is thinking that your
restraint file specifications are part of the group input.
> 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
> ntr = 1
> nmropt=1,
> /
> &ewald
> nfft1 = 90,
> nfft2 = 90,
> nfft3 = 90
> /
> &end
This &end should not be here.
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
> /
Neither should this /
Here is what is happening (I think): the input file parser thinks it has
found a "&end" namelist that you've defined. However, no part of your
simulation demands a &end namelist, so it is not read, but it's also not
tagged as the group input section (which is what it is). Therefore, the
parser tries to parse the part of the input file below as the GROUP
input for the restraints.
Long story short, remove the &end and / that I tagged above, and it
should win.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 29 2012 - 07:00:03 PDT
