------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 01/02/2015 at 12:34:05 [-O]verwriting output File Assignments: | MDIN: tgtmd3.in | MDOUT: tmdoTOc20.out |INPCRD: open1_md2.crd | PARM: open.top |RESTRT: restrt | REFC: closed1_md2.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: TMD: open->closed; target rmsd 1.6; resid 38-134 restrained &cntrl imin = 0, ntx = 1, nstlim = 5000, irest = 0, dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001, temp0 = 300.0, cut = 10.0, ntpr = 1, ntwx = 50, ntwr = 50, ntb = 0, ntt = 1, tautp = 0.5, ntp = 0, igb = 1, nscm = 0, nmropt = 1, ntr = 1, restraint_wt = 0.02, restraintmask = ":38-58,62-85,104-134", itgtmd = 1, tgtrmsd = 1.6, tgtmdfrc = 1.0, tgtrmsmask = "(:1-37,59-61,86-103)", / &wt TYPE='TGTRMSD', istep1=1, istep2=1000, value1 = 1.000, value2 = 0.0, / &wt TYPE='TGTRMSD', istep1=1000, istep2=0, value1 = 0.0, value2 = 0.0, / &wt type='END', / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 12/16/14 Time = 11:09:22 NATOM = 65142 NTYPES = 16 NBONH = 64099 MBONA = 1054 NTHETH = 2507 MTHETA = 1426 NPHIH = 4780 MPHIA = 3642 NHPARM = 0 NPARM = 0 NNB = 95858 NRES = 21135 NBONA = 1054 NTHETA = 1426 NPHIA = 3642 NUMBND = 34 NUMANG = 67 NPTRA = 36 NATYP = 25 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 3843812 | Hollerith 216563 | Integer 1224175 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 35657 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 50 iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 5000, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 0.00000, tautp = 0.50000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Targeted molecular dynamics: tgtrmsd = 1.60000, tgtmdfrc= 1.00000 | INFO: Old style inpcrd file read