AMBER Archive (2005)

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

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue May 31 2005 - 14:02:46 CDT


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 > > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu