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-- Guanglei L Jin wrote: > 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 >>> >>> >>> >>>----------------------------------------------------------------------- >>>The AMBER Mail Reflector >>>To post, send mail to amber.scripps.edu >>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> >>----------------------------------------------------------------------- >>The AMBER Mail Reflector >>To post, send mail to amber.scripps.edu >>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> > > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu