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

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Sun, 1 Apr 2012 20:18:20 +0200

Dear Jason

Thank you very much.
I wrote this new input, but it still does not work, and amber reads only
the input and it does not go on

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

 /

 Keep DNA fixed with weak restraints

 0.05

 RES 1 48

 END

 END

 /

 &wt type=DUMPFREQ, istep1=1,

 /

 &wt type='END',

 /

 DISANG=dist_chi.RST

 DUMPAVE=restraint.log

 LISTIN=POUT

 LISTOUT=POUT

 /

 &ewald

 nfft1 = 90,

 nfft2 = 90,

 nfft3 = 90



the dist_chi.RST is the following

&rst iat=-1,-1,
         ninc=0,ir6=0,ifntyp=0,nstep1=1,nstep2=100000,
   r1=0.0000E+00,r2=18.0000,r3=18.0000,r4=100.000,rk2=5,rk3=5,
       igr1 =
157,158,159,160,161,164,166,167,169,170,172,173,174,175,178,179,181,182,183,185,188,189,190,191
,192,193,196,198,199,201,202,204,205,209,210,211,213,214,215,217,220,536,537,538,539,540,543,545,546,548,549,55
1,552,553,554,557,558,560,561,562,564,567,568,569,570,571,572,575,577,578,580,581,583,584,588,589,590,594,596,5
99,
       igr2 =
915,916,917,918,919,922,924,925,927,928,930,931,932,933,936,937,940,941,943,946,947,948,949,950
,951,954,956,957,959,960,962,963,967,968,969,971,972,973,975,978,1294,1295,1296,1297,1298,1301,1303,1304,1306,1
307,1309,1310,1311,1312,1315,1316,1319,1320,1322,1325,1326,1327,1328,1329,1330,1333,1335,1336,1338,1339,1341,13
42,1346,1347,1348,1350,1351,1352,1354,1357/

2012/4/1 Jason Swails <jason.swails.gmail.com>

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
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 - 11:30:03 PDT
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