1 2 ------------------------------------------------------- 3 Amber 9 SANDER 2006 4 ------------------------------------------------------- 5 6| Run on 09/24/2007 at 15:22:46 7 [-O]verwriting output 8 9File Assignments: 10| MDIN: iapbs.in 11| MDOUT: iapbs.3.parse.out 12|INPCRD: pgb.rst 13| PARM: prmtop 14|RESTRT: restrt 15| REFC: refc 16| MDVEL: mdvel 17| MDEN: mden 18| MDCRD: mdcrd 19|MDINFO: mdinfo 20|INPDIP: inpdip 21|RSTDIP: rstdip 22 23 24 Here is the input file: 25 26 test of PB reaction field on protein g solvated in a sphere (iAPBS) 27&cntrl 28 ntx=1, irest=0, 29 imin=1, ntmin=2, maxcyc=0, 30 ntpr=1, igb=6, ntb=0, 31 ntc=1, ntf=1, tol=0.000001, 32 / 33&apbs 34 apbs_debug=0, apbs_print=1, 35 grid = 0.5, 0.5, 0.5, 36 calc_type=0, cmeth=1, 37 bcfl=2, srfm=0, 38 chgm=0, srad =1.4, swin =0.3, 39 pdie=1.0, sdie=80.0, 40 calcforce=0, 41 radiopt=3, pqr='pgb-parse.pqr', 42&end 43 44-------------------------------------------------------------------------------- 45 1. RESOURCE USE: 46-------------------------------------------------------------------------------- 47 48| Flags: 49| New format PARM file being parsed. 50| Version = 1.000 Date = 03/08/04 Time = 15:34:25 51 NATOM = 855 NTYPES = 13 NBONH = 419 MBONA = 442 52 NTHETH = 951 MTHETA = 600 NPHIH = 1716 MPHIA = 1040 53 NHPARM = 0 NPARM = 0 NNB = 4698 NRES = 56 54 NBONA = 442 NTHETA = 600 NPHIA = 1040 NUMBND = 30 55 NUMANG = 65 NPTRA = 26 NATYP = 21 NPHB = 0 56 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 57 NCOPY = 0 58 59 60| Memory Use Allocated 61| Real 55051 62| Hollerith 5188 63| Integer 61665 64| Max Pairs 1 65| nblistReal 0 66| nblist Int 0 67| Total 691 kbytes 68| Duplicated 0 dihedrals 69| Duplicated 0 dihedrals 70 71-------------------------------------------------------------------------------- 72 2. CONTROL DATA FOR THE RUN 73-------------------------------------------------------------------------------- 74 75 76 77General flags: 78 imin = 1, nmropt = 0 79 80Nature and format of input: 81 ntx = 1, irest = 0, ntrx = 1 82 83Nature and format of output: 84 ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 85 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 86 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 87 88Potential function: 89 ntf = 1, ntb = 0, igb = 6, nsnb = 25 90 ipol = 0, gbsa = 0, iesp = 0 91 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 92 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 93 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 94 rdt = 0.00000, rgbmax = 25.00000 95 alpb = 0 96 scnb = 2.00000, scee = 1.20000 97 98Frozen or restrained atoms: 99 ibelly = 0, ntr = 0 100 101Energy minimization: 102 maxcyc = 0, ncyc = 10, ntmin = 2 103 dx0 = 0.01000, drms = 0.00010 104| INFO: Old style inpcrd file read 105 106 107-------------------------------------------------------------------------------- 108 3. ATOMIC COORDINATES AND VELOCITIES 109-------------------------------------------------------------------------------- 110 111 112 begin time read from input coords = 0.000 ps 113 114iAPBS: Initializing APBS interface 115iAPBS: Reading radii definition from pqr filename: pgb-parse.pqr 116iAPBS: Grid dime not specified, calculating ... 117iAPBS: Requesting recalculating dime during caclulations. 118iAPBS: Grid values: 119fglen: 39.487 53.381 51.722 120cglen: 39.487 56.747 53.927 121dime: 65 97 97 122grid: 0.500 0.500 0.500 123Required memory (in MB): 116.651 124 125 APBS calculation parameters: 126 127Nonlinear traditional PBE 128Multiple Debye-Huckel boundary conditions 129Molecular surface definition 130Using trilinear interpolation (linear splines) 131Grid dimension: 65 97 97 132Coarse grid lengths: 39.487 56.747 53.927 133Fine grid lengths: 39.487 53.381 51.722 134Grid spacings: 0.500 0.500 0.500 135Solute dielectric (pdie): 1.000 136Solvent dielectric (sdie): 80.000 137Temperature: 298.150 138sdens: 10.000 139Surface tension: 0.105 140radiopt is set to 3 141 142 Number of triangulated 3-point waters found: 0 143 144-------------------------------------------------------------------------------- 145 4. RESULTS 146-------------------------------------------------------------------------------- 147 148 149 150 NSTEP ENERGY RMS GMAX NAME NUMBER 151 1 -2.3064E+03 2.8943E+00 2.2881E+01 CG 606 152 153 BOND = 15.9232 ANGLE = 72.0306 DIHED = 259.6946 154 VDWAALS = -400.2516 EEL = -4454.9764 EPB = -1132.0474 155 1-4 VDW = 182.2148 1-4 EEL = 3058.2617 RESTRAINT = 0.0000 156 ENPOLAR = 92.7357 157 158 159 Maximum number of minimization cycles reached. 160 161 162 FINAL RESULTS 163 164 165 166 NSTEP ENERGY RMS GMAX NAME NUMBER 167 1 -2.3064E+03 2.8943E+00 2.2881E+01 CG 606 168 169 BOND = 15.9232 ANGLE = 72.0306 DIHED = 259.6946 170 VDWAALS = -400.2516 EEL = -4454.9764 EPB = -1132.0474 171 1-4 VDW = 182.2148 1-4 EEL = 3058.2617 RESTRAINT = 0.0000 172 ENPOLAR = 92.7357 173 174-------------------------------------------------------------------------------- 175 5. TIMINGS 176-------------------------------------------------------------------------------- 177 178| Read coords time 0.00 ( 0.02% of Total) 179| Calc gb off-diag 0.01 (99.85% of Gen B) 180| Other 0.00 ( 0.15% of Gen B) 181| Gen Born time 0.01 ( 0.02% of Nonbo) 182| PB Nonbond 23.68 (100.0% of Nonbo) 183| Nonbond force 23.69 (100.0% of Force) 184| Force time 23.69 (100.0% of Runmd) 185| Runmd Time 23.69 (100.0% of Total) 186| Other 0.01 ( 0.06% of Total) 187| Total time 23.71 (100.0% of ALL ) 188 189| Highest rstack allocated: 0 190| Highest istack allocated: 0 191| Job began at 15:22:46.772 on 09/24/2007 192| Setup done at 15:22:46.787 on 09/24/2007 193| Run done at 15:23:10.479 on 09/24/2007 194| wallclock() was called 22 times 195