------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 04/18/2007 at 13:19:55 [-O]verwriting output File Assignments: | MDIN: min4.in | MDOUT: 4hdp_min4.out |INPCRD: 4hdp_min1.rst7 | PARM: 4hdp.top |RESTRT: 4hdp_min4.rst7 | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Full Minimization run &cntrl imin=1, ntb=1, ntr =0, maxcyc=5000, ncyc = 250, ntpr = 50, ntwr = 1000, cut = 10 / END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 38.547 | New format PARM file being parsed. | Version = 1.000 Date = 04/17/07 Time = 09:41:03 NATOM = 56737 NTYPES = 21 NBONH = 53353 MBONA = 3515 NTHETH = 7236 MTHETA = 4858 NPHIH = 13668 MPHIA = 8996 NHPARM = 0 NPARM = 0 NNB = 103245 NRES = 17121 NBONA = 3515 NTHETA = 4858 NPHIA = 8996 NUMBND = 89 NUMANG = 182 NPTRA = 65 NATYP = 58 NPHB = 1 IFBOX = 2 NMXRS = 41 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 4653004 | Hollerith 357545 | Integer 3742702 | Max Pairs 32680512 | Max Rstack 3451230 | Max Istack 283685 | Total 208097 kbytes | 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 = 1000 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 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 5000, ncyc = 250, 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 = 94.421 Box Y = 94.421 Box Z = 94.421 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 96 NFFT2 = 96 NFFT3 = 96 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 16720 | Atom division among processors: | 0 56737 | Running AMBER/MPI version on 1 nodes Sum of charges from parm topology file = 0.00003987 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 = 0.3338E-14 at 2.509280 | CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 18054823 | TOTAL SIZE OF NONBOND LIST = 18054823 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.2321E+05 3.8953E+00 4.2588E+02 H5'2 5997 BOND = 16916.2571 ANGLE = 1739.4880 DIHED = 4096.5554 VDWAALS = 40862.3996 EEL = -297516.9514 HBOND = 0.0000 1-4 VDW = 1560.6806 1-4 EEL = 9135.7890 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -2.2572E+05 7.3937E-01 1.2586E+02 C2 6558 BOND = 16890.2550 ANGLE = 1211.4982 DIHED = 4028.7387 VDWAALS = 39862.8017 EEL = -297678.1053 HBOND = 0.0000 1-4 VDW = 1413.7225 1-4 EEL = 8549.7243 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -2.2601E+05 3.0268E-01 2.5459E+01 C4 6561 BOND = 16887.8782 ANGLE = 1147.6534 DIHED = 4008.8534 VDWAALS = 39826.4452 EEL = -297791.2163 HBOND = 0.0000 1-4 VDW = 1394.5407 1-4 EEL = 8517.3719 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -2.2614E+05 5.5414E-01 4.6434E+01 C2 6558 BOND = 16901.5426 ANGLE = 1136.7589 DIHED = 3998.4318 VDWAALS = 39816.6895 EEL = -297879.0177 HBOND = 0.0000 1-4 VDW = 1385.6284 1-4 EEL = 8498.2752 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -2.2624E+05 3.3818E-01 2.8864E+01 C4 6561 BOND = 16901.1951 ANGLE = 1130.6813 DIHED = 3989.4681 VDWAALS = 39821.0926 EEL = -297952.8237 HBOND = 0.0000 1-4 VDW = 1381.2101 1-4 EEL = 8485.1576 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -2.2632E+05 1.7756E-01 1.2580E+01 C2 6558 BOND = 16906.4653 ANGLE = 1130.0267 DIHED = 3981.4300 VDWAALS = 39827.5755 EEL = -298021.0948 HBOND = 0.0000 1-4 VDW = 1377.1544 1-4 EEL = 8475.4903 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -2.2673E+05 2.6250E-01 1.7731E+01 CB 3927 BOND = 16947.3677 ANGLE = 1155.6015 DIHED = 3941.8589 VDWAALS = 39958.4980 EEL = -298493.6893 HBOND = 0.0000 1-4 VDW = 1368.3834 1-4 EEL = 8388.8515 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -2.2686E+05 2.1552E-01 1.6046E+01 HG23 3932 BOND = 16959.6522 ANGLE = 1145.1662 DIHED = 3929.8819 VDWAALS = 39996.9863 EEL = -298648.1989 HBOND = 0.0000 1-4 VDW = 1368.2847 1-4 EEL = 8387.6112 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -2.2696E+05 3.6179E-01 2.9945E+01 CG 3625 BOND = 16974.6158 ANGLE = 1150.5603 DIHED = 3920.5539 VDWAALS = 40040.0042 EEL = -298796.5155 HBOND = 0.0000 1-4 VDW = 1369.2206 1-4 EEL = 8377.0931 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -2.2707E+05 3.2404E-01 2.9674E+01 C4 6561 BOND = 16984.6525 ANGLE = 1157.3209 DIHED = 3912.1144 VDWAALS = 40091.2065 EEL = -298953.3824 HBOND = 0.0000 1-4 VDW = 1369.3208 1-4 EEL = 8369.4852 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.2717E+05 2.6034E-01 1.9138E+01 C4 6561 BOND = 16992.5244 ANGLE = 1152.8363 DIHED = 3905.8104 VDWAALS = 40126.8192 EEL = -299081.2729 HBOND = 0.0000 1-4 VDW = 1364.4862 1-4 EEL = 8368.7461 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 550 -2.2726E+05 2.7534E-01 1.9116E+01 C4 6561 BOND = 17001.8974 ANGLE = 1153.9918 DIHED = 3900.2223 VDWAALS = 40172.5267 EEL = -299209.4747 HBOND = 0.0000 1-4 VDW = 1362.2936 1-4 EEL = 8363.5247 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -2.2733E+05 2.2556E-01 1.3442E+01 CB 3927 BOND = 17008.5893 ANGLE = 1151.9729 DIHED = 3895.2269 VDWAALS = 40207.2826 EEL = -299312.4205 HBOND = 0.0000 1-4 VDW = 1359.8453 1-4 EEL = 8361.3039 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 650 -2.2739E+05 2.0401E-01 1.2811E+01 CA 3939 BOND = 17015.6825 ANGLE = 1152.4198 DIHED = 3890.9265 VDWAALS = 40240.4306 EEL = -299410.9314 HBOND = 0.0000 1-4 VDW = 1359.0368 1-4 EEL = 8357.7436 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -2.2747E+05 3.0587E-01 3.2872E+01 C2 6558 BOND = 17026.4534 ANGLE = 1156.0506 DIHED = 3886.6505 VDWAALS = 40282.4164 EEL = -299529.7804 HBOND = 0.0000 1-4 VDW = 1359.6636 1-4 EEL = 8352.5302 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -2.2754E+05 2.5768E-01 1.8696E+01 C2 6558 BOND = 17033.7335 ANGLE = 1155.3808 DIHED = 3882.2204 VDWAALS = 40320.3051 EEL = -299644.4903 HBOND = 0.0000 1-4 VDW = 1358.4285 1-4 EEL = 8349.7371 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -2.2770E+05 3.4381E-01 4.4577E+01 H1 20697 BOND = 17060.1647 ANGLE = 1161.8048 DIHED = 3874.2947 VDWAALS = 40426.4389 EEL = -299925.3982 HBOND = 0.0000 1-4 VDW = 1357.7419 1-4 EEL = 8346.1254 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 850 -2.2782E+05 2.8487E-01 1.8584E+01 H1 20697 BOND = 17073.3493 ANGLE = 1156.0576 DIHED = 3867.0246 VDWAALS = 40464.5408 EEL = -300080.5948 HBOND = 0.0000 1-4 VDW = 1355.9279 1-4 EEL = 8346.2641 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -2.2788E+05 2.1082E-01 1.4861E+01 O 20795 BOND = 17072.8595 ANGLE = 1154.3251 DIHED = 3864.4877 VDWAALS = 40486.2323 EEL = -300152.4498 HBOND = 0.0000 1-4 VDW = 1353.6402 1-4 EEL = 8340.4735 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 950 -2.2793E+05 1.9771E-01 9.9773E+00 CB 1083 BOND = 17079.0040 ANGLE = 1154.3490 DIHED = 3862.2195 VDWAALS = 40512.3421 EEL = -300228.8516 HBOND = 0.0000 1-4 VDW = 1352.8010 1-4 EEL = 8336.8915 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -2.2798E+05 1.9059E-01 1.7260E+01 CB 4013 BOND = 17085.7602 ANGLE = 1156.2814 DIHED = 3860.2901 VDWAALS = 40541.9743 EEL = -300312.1734 HBOND = 0.0000 1-4 VDW = 1352.8177 1-4 EEL = 8332.5594 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1050 -2.2804E+05 1.9700E-01 1.6269E+01 CG 4880 BOND = 17093.7169 ANGLE = 1158.5986 DIHED = 3858.3783 VDWAALS = 40571.6935 EEL = -300399.9917 HBOND = 0.0000 1-4 VDW = 1353.0102 1-4 EEL = 8327.7942 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1100 -2.2815E+05 2.8181E-01 2.2025E+01 CG 4880 BOND = 17114.9548 ANGLE = 1171.5502 DIHED = 3855.6769 VDWAALS = 40639.5840 EEL = -300598.4684 HBOND = 0.0000 1-4 VDW = 1353.9459 1-4 EEL = 8313.8344 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1150 -2.2823E+05 2.1816E-01 1.8657E+01 CG 4880 BOND = 17121.8230 ANGLE = 1164.0013 DIHED = 3852.3271 VDWAALS = 40661.6254 EEL = -300695.9080 HBOND = 0.0000 1-4 VDW = 1350.7648 1-4 EEL = 8312.1187 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1200 -2.2827E+05 2.0917E-01 1.8315E+01 CG 4880 BOND = 17126.3576 ANGLE = 1167.9018 DIHED = 3850.6106 VDWAALS = 40675.6904 EEL = -300750.1756 HBOND = 0.0000 1-4 VDW = 1350.3210 1-4 EEL = 8304.6394 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1250 -2.2832E+05 2.3778E-01 1.7605E+01 CG 4880 BOND = 17133.4240 ANGLE = 1182.5477 DIHED = 3849.3116 VDWAALS = 40689.9653 EEL = -300805.8532 HBOND = 0.0000 1-4 VDW = 1350.6664 1-4 EEL = 8281.6934 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1300 -2.2773E+05 2.7662E+00 7.6959E+02 H1 6532 BOND = 17501.0969 ANGLE = 1337.3969 DIHED = 3852.8853 VDWAALS = 40722.4577 EEL = -300784.9482 HBOND = 0.0000 1-4 VDW = 1347.8395 1-4 EEL = 8291.1743 RESTRAINT = 0.0000