------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Fri Jun 11 10:47:00 2004 [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: ttr_min_wat.out |INPCRD: ttr.crd | PARM: ttr.top |RESTRT: ttr_min.rst | REFC: ttr.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization with Cartesian restraints for the solute &cntrl imin=1, maxcyc=200, ntpr=5, ntr=1, ncyc=500, &end Group input for restrained atoms 100.0 RES 1 458 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found | New format PARM file being parsed. | Version = 1.000 Date = 06/11/04 Time = 10:37:02 NATOM = 48869 NTYPES = 17 NBONH = 45309 MBONA = 3636 NTHETH = 7846 MTHETA = 4962 NPHIH = 14758 MPHIA = 9196 NHPARM = 0 NPARM = 0 NNB = 94536 NRES = 14425 NBONA = 3636 NTHETA = 4962 NPHIA = 9196 NUMBND = 45 NUMANG = 91 NPTRA = 40 NATYP = 32 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated Used | Real 6000000 4014483 | Hollerith 800000 307641 | Integer 6000000 3870533 | Max Nonbonded Pairs:10800000 | 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 = 1 Energy minimization: maxcyc = 200, ncyc = 500, 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 = 72.535 Box Y = 104.558 Box Z = 80.400 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 108 NFFT3 = 80 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: Group input for restrained atoms GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000 GRP 1 RES 1 TO 458 Number of atoms in this group = 7000 ----- 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: 13951 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 = 0.3242E-14 at 2.436720 | CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 8412681 | TOTAL SIZE OF NONBOND LIST = 8412681 NSTEP ENERGY RMS GMAX NAME NUMBER 1 NAN NAN 6.4076E+04 C 6998 BOND = 4558117.6476 ANGLE = 1310.8486 DIHED = 3688.2075 VDWAALS = nan EEL = nan HBOND = 0.0000 1-4 VDW = 2028.5963 1-4 EEL = 22119.3049 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 10 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 15 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 20 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 25 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 30 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 35 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 40 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 45 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 50 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan NSTEP ENERGY RMS GMAX NAME NUMBER 55 NAN NAN 0.0000E+00 N 1 BOND = nan ANGLE = nan DIHED = nan VDWAALS = -1315.8256 EEL = nan HBOND = 0.0000 1-4 VDW = nan 1-4 EEL = nan RESTRAINT = nan EAMBER = nan