AMBER Archive (2005)

Subject: AMBER: Error on restrained MD equilibration (AMBER 7)

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue May 31 2005 - 10:23:51 CDT


Dear Amber users,

I am running a MD equilibration to heat up the system from 0 to 300K while
restrained the solute weakly with the following input file. But there is an
error message about decoding the variable in the input file, which seems to be
something related to the variable 'ntr = 1'. If I changed 'ntr = 1' to 'ntr =
0' the output was OK but that would not restrain the solute. Could anybody
indicate any mistake I have made? Many thanks

INPUT:

MD heating from 0 to 300K with restraints on the solute
 &cntrl
   imin = 0, ntpr = 100, ntwx = 100, ntwe = 100, ntwr = 1000,
   nstlim =10000, dt = 0.001,
   ntb = 1,cut = 8, ntr = 1, ntc = 2, ntf = 2, nmropt = 1,
   tempi = 0.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
 &end
&wt
   type='TEMP0', istep1=0, istep2=500,
                 value1=0.0, value2=300.0,
  &end
  &wt
   type='TEMP0', istep1=500, istep2=20000,
                 value1=300.0, value2=300.0,
  &end
  &wt
   type='END',
  &end
Group input for restraint atoms
 10
RES 1
END
END

OUTPUT:

.....................................

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Molecular dynamics:
     nstlim = 10000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000

Temperature regulation:
     ig = 71277, ntt = 1, vrand = 0
     temp0 = 300.00000, tempi = 0.00000, heat = 0.00000
     dtemp = 5.00000, tautp = 0.50000

SHAKE:
     ntc = 2, jfastw = 0
     tol = 0.00001

NMR refinement options:
     iscale = 0, noeskp = 1, ipnlty = 1, mxcub = 1
     scalm = 100.00000, pencut = 0.10000, tausw = 0.10000

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
     Box X = 41.027 Box Y = 40.420 Box Z = 40.470
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 48 NFFT2 = 40 NFFT3 = 40
     Cutoff= 8.000 Tol =0.100E-04
     Ewald Coefficient = 0.34864
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
 MD heating from 0 to 300K with restraints on the solute

     rfree: Error decoding variable 1 3 from:
 &cntrl

Lan

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