------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 06/27/2006 at 12:37:01 [-O]verwriting output File Assignments: | MDIN: 1cgh-hold-protein.in | MDOUT: 1cgh-hold-protein.out |INPCRD: 1cgh-water-box.crd | PARM: 1cgh-water-box.top |RESTRT: 1cgh-hold-protein.rst | REFC: 1cgh-water-box.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: 1cgh: initial minimization of solvent and ions &cntrl imin = 1, maxcyc = 500, ncyc = 250, ntb = 1, ntr = 1, cut = 10 &end Hold the protein fixed 100.0 RES 1 228 END END -------------------------------------------------------------------------------- 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 = 31.092 | New format PARM file being parsed. | Version = 1.000 Date = 06/27/06 Time = 12:16:52 NATOM = 29776 NTYPES = 18 NBONH = 27929 MBONA = 1859 NTHETH = 4126 MTHETA = 2513 NPHIH = 7341 MPHIA = 3511 NHPARM = 0 NPARM = 0 NNB = 54902 NRES = 8953 NBONA = 1859 NTHETA = 2513 NPHIA = 3511 NUMBND = 46 NUMANG = 100 NPTRA = 38 NATYP = 31 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2511440 | Hollerith 187611 | Integer 1948727 | Max Pairs 17150976 | Max Rstack 1929334 | Max Istack 148880 | Total 110616 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 = 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 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 500, 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 = 76.158 Box Y = 76.158 Box Z = 76.158 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 80 NFFT2 = 80 NFFT3 = 80 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 100.00000 GRP 1 RES 1 TO 228 Number of atoms in this group = 3655 ----- 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: 8698 Sum of charges from parm topology file = -0.00000025 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 = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 9440573 | TOTAL SIZE OF NONBOND LIST = 9440573 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -3.9473E+04 8.1264E+02 6.1082E+04 O 25343 BOND = 382.7742 ANGLE = 711.5484 DIHED = 376.1588 VDWAALS = 49971.5658 EEL = -96858.6339 HBOND = 0.0000 1-4 VDW = 1119.9428 1-4 EEL = 4824.1408 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 50 -9.7981E+04 1.5980E+00 1.8340E+01 Cl- 3662 BOND = 5242.8720 ANGLE = 538.9913 DIHED = 373.7434 VDWAALS = 6977.7009 EEL = -117106.3797 HBOND = 0.0000 1-4 VDW = 1025.2987 1-4 EEL = 4676.5648 RESTRAINT = 289.9003 EAMBER = -98271.2087 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.0228E+05 9.8533E-01 2.2588E+01 C 3633 BOND = 5458.7665 ANGLE = 536.3727 DIHED = 372.7286 VDWAALS = 7801.0902 EEL = -122438.6097 HBOND = 0.0000 1-4 VDW = 1025.1114 1-4 EEL = 4677.1011 RESTRAINT = 282.4839 EAMBER = -102567.4393 NSTEP ENERGY RMS GMAX NAME NUMBER 150 -1.0444E+05 1.2249E+00 9.4737E+01 C1 3595 BOND = 5802.3803 ANGLE = 537.8920 DIHED = 372.0062 VDWAALS = 8616.1053 EEL = -125755.8297 HBOND = 0.0000 1-4 VDW = 1025.2235 1-4 EEL = 4677.8474 RESTRAINT = 279.9607 EAMBER = -104724.3750 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.0586E+05 9.5256E-01 4.0272E+01 C 3633 BOND = 5997.4798 ANGLE = 538.6563 DIHED = 371.5306 VDWAALS = 9327.9811 EEL = -128079.9551 HBOND = 0.0000 1-4 VDW = 1023.9522 1-4 EEL = 4677.3072 RESTRAINT = 281.7024 EAMBER = -106143.0478 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -1.0692E+05 1.6818E+00 1.9191E+02 C1 3595 BOND = 6191.2413 ANGLE = 542.1344 DIHED = 371.1276 VDWAALS = 9975.4190 EEL = -129978.5848 HBOND = 0.0000 1-4 VDW = 1023.3854 1-4 EEL = 4676.8542 RESTRAINT = 281.8950 EAMBER = -107198.4229 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.1048E+05 1.8304E+00 1.3847E+02 H2 3805 BOND = 6886.6184 ANGLE = 551.8480 DIHED = 373.5366 VDWAALS = 13198.3302 EEL = -137503.5199 HBOND = 0.0000 1-4 VDW = 1026.8462 1-4 EEL = 4673.1857 RESTRAINT = 316.5405 EAMBER = -110793.1547 NSTEP ENERGY RMS GMAX NAME NUMBER 350 -1.1157E+05 1.3603E+00 1.0831E+02 O 21 BOND = 7078.9730 ANGLE = 553.2872 DIHED = 373.9520 VDWAALS = 13812.9913 EEL = -139391.7220 HBOND = 0.0000 1-4 VDW = 1024.0512 1-4 EEL = 4676.2900 RESTRAINT = 305.2183 EAMBER = -111872.1774 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.1262E+05 1.0417E+00 5.5017E+01 O 21 BOND = 7272.6677 ANGLE = 544.7546 DIHED = 371.2489 VDWAALS = 14678.0298 EEL = -141474.6891 HBOND = 0.0000 1-4 VDW = 1024.3383 1-4 EEL = 4675.7480 RESTRAINT = 284.5932 EAMBER = -112907.9017 NSTEP ENERGY RMS GMAX NAME NUMBER 450 -1.1349E+05 7.7598E-01 4.4697E+01 CD 1852 BOND = 7446.6132 ANGLE = 541.0895 DIHED = 371.3717 VDWAALS = 15345.2548 EEL = -143178.2393 HBOND = 0.0000 1-4 VDW = 1024.7575 1-4 EEL = 4676.4583 RESTRAINT = 281.1243 EAMBER = -113772.6944 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.1465E+05 7.5336E-01 4.9686E+01 O 21 BOND = 7689.8536 ANGLE = 537.5148 DIHED = 371.7255 VDWAALS = 16520.2259 EEL = -145753.1265 HBOND = 0.0000 1-4 VDW = 1023.7618 1-4 EEL = 4678.4369 RESTRAINT = 277.6182 EAMBER = -114931.6080 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.1465E+05 7.5336E-01 4.9686E+01 O 21 BOND = 7689.8536 ANGLE = 537.5148 DIHED = 371.7255 VDWAALS = 16520.2259 EEL = -145753.1265 HBOND = 0.0000 1-4 VDW = 1023.7618 1-4 EEL = 4678.4369 RESTRAINT = 277.6182 EAMBER = -114931.6080 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.08 ( 0.01% of Total) | Build the list 11.73 (96.44% of List ) | Other 0.43 ( 3.56% of List ) | List time 12.17 ( 1.91% of Nonbo) | Short_ene time 507.76 (99.25% of Direc) | Other 3.83 ( 0.75% of Direc) | Direct Ewald time 511.59 (81.86% of Ewald) | Adjust Ewald time 3.16 ( 0.51% of Ewald) | Fill Bspline coeffs 4.06 ( 3.73% of Recip) | Fill charge grid 12.65 (11.63% of Recip) | Scalar sum 29.31 (26.95% of Recip) | Grad sum 17.04 (15.67% of Recip) | FFT time 45.67 (42.00% of Recip) | Recip Ewald time 108.74 (17.40% of Ewald) | Force Adjust 0.75 ( 0.12% of Ewald) | Virial junk 0.49 ( 0.08% of Ewald) | Start sycnronization 0.18 ( 0.03% of Ewald) | Ewald time 624.93 (98.09% of Nonbo) | Nonbond force 637.09 (99.19% of Force) | Bond/Angle/Dihedral 4.90 ( 0.76% of Force) | Other 0.28 ( 0.04% of Force) | Force time 642.27 (100.0% of Runmd) | Runmd Time 642.27 (99.55% of Total) | Other 2.85 ( 0.44% of Total) | Total time 645.20 (100.0% of ALL ) | Highest rstack allocated: 1899802 | Highest istack allocated: 29776 | Job began at 12:37:01.568 on 06/27/2006 | Setup done at 12:37:02.207 on 06/27/2006 | Run done at 12:47:46.773 on 06/27/2006 | wallclock() was called 16526 times