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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Received on Tue May 31 2005 - 16:53:03 PDT
