Hi Guanglei,
Thank you for the suggestion but it does not work in my case. Could you send me
your input file if possible for me to find some clue?
Lan
Quoting Guanglei Cui <cuigl.csb.sunysb.edu>:
> Hi,
>
> Try to put the following lines between your weight change section and
> the group input section. It may help. At least it works for me when
> nmropt and ntr are both used.
>
> LISTIN=POUT
> LISTOUT=POUT
>
> Regards,
>
> --
> Guanglei
>
> L Jin wrote:
> > 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
> >
> >
> >
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Received on Wed Jun 01 2005 - 11:53:00 PDT
