------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | Run on 12/02/2010 at 14:37:32 [-O]verwriting output File Assignments: | MDIN: in/min_sol.in | MDOUT: mdout |INPCRD: 1XCK_E461K_MGATP_sol.inpcrd | PARM: 1XCK_E461K_MGATP_sol_ONE.prmtop |RESTRT: restrt | REFC: 1XCK_E461K_MGATP_sol.inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: minimization of waters &cntrl imin = 1, maxcyc=8000, ncyc=5000, ntb=1, ntr=1, cut=10, / Hold the protein fixed 500.0 RES 1 7336 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 87.894 | New format PARM file being parsed. | Version = 1.000 Date = 12/01/10 Time = 18:01:57 NATOM = 719366 NTYPES = 20 NBONH = 665158 MBONA = 54607 NTHETH = 127652 MTHETA = 73780 NPHIH = 238210 MPHIA = 173474 NHPARM = 0 NPARM = 0 NNB = 1419358 NRES = 210440 NBONA = 54607 NTHETA = 73780 NPHIA = 173474 NUMBND = 54 NUMANG = 108 NPTRA = 66 NATYP = 38 NPHB = 1 IFBOX = 2 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 46126995 | Hollerith 2368540 | Integer 35995957 | Max Pairs 414354816 | nblistReal 8632392 | nblist Int 24755567 | Total 2292943 kbytes | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 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 = 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 = 10.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 8000, ncyc = 5000, 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 = 0 Box X = 215.296 Box Y = 215.296 Box Z = 215.296 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 216 NFFT2 = 216 NFFT3 = 216 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the protein fixed GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000 GRP 1 RES 1 TO 7336 Number of atoms in this group = ***** ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 203090 Sum of charges from parm topology file = ************ Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 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 = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 243081978 | TOTAL SIZE OF NONBOND LIST = 243081978 NSTEP ENERGY RMS GMAX NAME NUMBER 1 1.1987E+07 2.0862E+05 2.0910E+08 O 112587 BOND = 2189.1380 ANGLE = 12050.6822 DIHED = 66005.0153 VDWAALS = 14068995.3440 EEL = -2550501.5293 HBOND = 0.0000 1-4 VDW = 40310.0018 1-4 EEL = 347476.6719 RESTRAINT = 0.0000