Re: [AMBER] rfree: Error decoding variable 1 3 from:

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Sun, 1 Apr 2012 18:53:03 +0200

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
 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


thank you

Elisa

2012/3/29 Jason Swails <jason.swails.gmail.com>

> 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
>
>


-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
UniversitÓ di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
         elisa.frezza.studenti.unipd.it
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Received on Sun Apr 01 2012 - 10:00:02 PDT
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