Thank you all for the help. I have tried to specify the group as a range and
also using the right format of the namelist record. But it still gave the same
error. I just need to restrain residue 1, a small molecule, in the water box to
equilibrate the solvent. Anything else we could consider?
Cheers,
Lan
> 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 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue May 31 2005 - 17:53:00 PDT
