------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 03/12/2008 at 15:54:49 [-O]verwriting output File Assignments: | MDIN: min1.in | MDOUT: min2.out |INPCRD: aib1meth.inpcrd | PARM: aib1meth.prmtop |RESTRT: min1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: minimisation of model system &cntrl imin = 1, maxcyc = 1000, ncyc = 1000, cut = 2.5, lastrst = 80000000 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 4.964 | New format PARM file being parsed. | Version = 1.000 Date = 03/12/08 Time = 13:47:16 NATOM = 56 NTYPES = 11 NBONH = 29 MBONA = 27 NTHETH = 62 MTHETA = 36 NPHIH = 92 MPHIA = 67 NHPARM = 0 NPARM = 0 NNB = 279 NRES = 2 NBONA = 27 NTHETA = 36 NPHIA = 67 NUMBND = 16 NUMANG = 29 NPTRA = 27 NATYP = 14 NPHB = 0 IFBOX = 1 NMXRS = 50 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 94286 | Hollerith 340 | Integer 73911 | Max Pairs 1540 | Max Rstack 7178 | Max Istack 280 | Total 1089 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- AIB General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 2.50000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 1000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 14.348 Box Y = 14.553 Box Z = 9.928 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 16 NFFT2 = 15 NFFT3 = 9 Cutoff= 2.500 Tol =0.100E-04 Ewald Coefficient = 1.19213 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- AIB begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00001000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- Exceeding lastrst in get_stack lastrst = 7178 top_stk= 0 isize = 22352 request= 22352 Increase lastrst in the &cntrl namelist