Hello,
I'm getting used to a new mail client, I apologize for replying
off-list. I'm moving it back to the list for now.
On Thu, 2012-03-29 at 16:07 +0200, Elisa Frezza wrote:
> I wrote the following input file but it does not work
>
>
> 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,
As Prof. Case mentioned, you need to set ntr=1 in your input file in
order to read the group input for cartesian restraints.
> /
> &ewald
> nfft1 = 90,
> nfft2 = 90,
> nfft3 = 90
You removed the closing of this namelist (/). Each namelist is
specified with a
&namelist_name
variable1=value1, variable2=value2,
variable3=value3,
/
Notice the &namelist_name and the / to start and end the namelist,
respectively. Each namelist for Amber (and any Fortran program that
takes a namelist input) must be specified this way.
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
> &wt type=DUMPFREQ, istep1=1, /
> &wt type=END &end
> DISANG=dist_chi.RST
> DUMPAVE=restraint.log
> LISTIN=POUT
> LISTOUT=POUT
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 - 12:00:04 PDT
