------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Mon Apr 2 05:18:18 2007 [-O]verwriting output File Assignments: | MDIN: min1a.in | MDOUT: 2c17mul1min1.out |INPCRD: 2c17mul1.inpcrd | PARM: 2c17mul1.prmtop |RESTRT: 2c17mul1min1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization solvates with cartesian restriantes for the solute &cntrl imin=1, ncyc=250, maxcyc=1000, ntpr=5, &end Group input for restrained atoms 10.0 RES 1 454 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MEM_ALLOC HAS_FTN_ERFC NO_SIGN getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found | New format PARM file being parsed. | Version = 1.000 Date = 04/02/07 Time = 05:06:23 NATOM = 53499 NTYPES = 17 NBONH = 49878 MBONA = 3697 NTHETH = 8378 MTHETA = 5005 NPHIH = 14972 MPHIA = 8381 NHPARM = 0 NPARM = 0 NNB = 102036 NRES = 15857 NBONA = 3697 NTHETA = 5005 NPHIA = 8381 NUMBND = 45 NUMANG = 91 NPTRA = 32 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated | Real 4172538 | Hollerith 336853 | Integer 4156992 | Max Pairs 15285428 | Max Rstack 2000000 | Max Istack 2000000 | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 5, 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 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1000, ncyc = 250, ntmin = 1 dx0 = 0.01000, dxm = 0.50000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1 Box X = 96.129 Box Y = 76.278 Box Z = 90.199 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 96 NFFT2 = 80 NFFT3 = 90 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 15402 Sum of charges from parm topology file = -0.00000020 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.1990E-14 at 2.461500 | CHECK d/dx switch(x): max rel err = 0.7670E-11 at 2.772760 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 9287199 | TOTAL SIZE OF NONBOND LIST = 9287199 Exceeding lastrst lastrst = 2000000 top_stk= 1840755 isize = 213996 request= 2054751 Increase lastrst in the &cntrl namelist