On Sun, 2012-04-01 at 18:53 +0200, Elisa Frezza wrote:
> Hello thank you for your answer, but I do not understand what name I
> have to put to cartesian restraints because the program always reads
> the file where I put nmr restraints. I delete / and &end, but the
> error persists.
>
>
> Here there is my new input 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,
> &namelist_name
This is not correct. You've effectively started a new namelist (titled
'namelist_name') in the middle of your &ewald namelist, but failed to
end either "namelist_name" or "ewald". Every namelist that you start
MUST be ended with either / or &end (I suggest just using / ). Amber
recognizes several namelists, including &cntrl &pb &qmmm &ewald &wt
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
> &wt type=DUMPFREQ, istep1=1, /
> &wt type=END &end
DUMPFREQ and END must be put in quotes, since you need to match the
string, not a variable.
Note, after making the suggested changes above, the input file worked
for me (it just died when trying to open dist_chi.RST, since I don't
have that file, but you should).
HTH,
Jason
--
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 - 11:30:03 PDT
