1 2 ------------------------------------------------------- 3 Amber 9 SANDER 2006 4 ------------------------------------------------------- 5 6| Run on 09/24/2007 at 22:04:50 7 [-O]verwriting output 8 9File Assignments: 10| MDIN: solvation.in 11| MDOUT: Ba 12|INPCRD: 2ala.prmcrd 13| PARM: 2ala.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 26APBS solvation energy example 27&cntrl 28 maxcyc=0, imin=1, 29 cut=12.0, 30 igb=6, ntb=0, 31 ntpr=1, 32 / 33&apbs 34 apbs_debug=9, 35 apbs_print=1, 36 grid=0.5, 0.5, 0.5, 37 calc_type=0, 38 cmeth=1, 39 bcfl=2, 40 srfm=1, 41 chgm=1, 42 pdie=1.0, 43 sdie=78.54, 44 srad = 1.4, 45 radiopt=3, pqr='2ala.pqr', 46 calcforce=0, calcnpenergy=1, 47&end 48 49-------------------------------------------------------------------------------- 50 1. RESOURCE USE: 51-------------------------------------------------------------------------------- 52 53| Flags: 54| New format PARM file being parsed. 55| Version = 1.000 Date = 10/18/06 Time = 21:21:36 56 NATOM = 22 NTYPES = 7 NBONH = 12 MBONA = 9 57 NTHETH = 25 MTHETA = 11 NPHIH = 42 MPHIA = 18 58 NHPARM = 0 NPARM = 0 NNB = 99 NRES = 3 59 NBONA = 9 NTHETA = 11 NPHIA = 18 NUMBND = 8 60 NUMANG = 16 NPTRA = 16 NATYP = 7 NPHB = 0 61 IFBOX = 0 NMXRS = 10 IFCAP = 0 NEXTRA = 0 62 NCOPY = 0 63 64 Implicit solvent radii are modified Bondi radii (mbondi) 65 66| Memory Use Allocated 67| Real 1592 68| Hollerith 137 69| Integer 21004 70| Max Pairs 1 71| nblistReal 0 72| nblist Int 0 73| Total 95 kbytes 74| Duplicated 0 dihedrals 75| Duplicated 0 dihedrals 76 77-------------------------------------------------------------------------------- 78 2. CONTROL DATA FOR THE RUN 79-------------------------------------------------------------------------------- 80 81ACE 82 83General flags: 84 imin = 1, nmropt = 0 85 86Nature and format of input: 87 ntx = 1, irest = 0, ntrx = 1 88 89Nature and format of output: 90 ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 91 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 92 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 93 94Potential function: 95 ntf = 1, ntb = 0, igb = 6, nsnb = 25 96 ipol = 0, gbsa = 0, iesp = 0 97 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 98 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 99 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 100 rdt = 0.00000, rgbmax = 25.00000 101 alpb = 0 102 scnb = 2.00000, scee = 1.20000 103 104Frozen or restrained atoms: 105 ibelly = 0, ntr = 0 106 107Energy minimization: 108 maxcyc = 0, ncyc = 10, ntmin = 1 109 dx0 = 0.01000, drms = 0.00010 110| INFO: Old style inpcrd file read 111 112 113-------------------------------------------------------------------------------- 114 3. ATOMIC COORDINATES AND VELOCITIES 115-------------------------------------------------------------------------------- 116 117ACE 118 begin time read from input coords = 0.000 ps 119 120iAPBS: Initializing APBS interface 121iAPBS: Reading radii definition from pqr filename: 2ala.pqr 122iAPBS: Grid dime not specified, calculating ... 123iAPBS: Requesting recalculating dime during caclulations. 124iAPBS: Grid values: 125fglen: 13.801 18.154 10.192 126cglen: 13.801 18.154 10.192 127dime: 33 33 33 128grid: 0.500 0.500 0.500 129Required memory (in MB): 6.854 130 131 APBS calculation parameters: 132 133Nonlinear traditional PBE 134Multiple Debye-Huckel boundary conditions 135Smoothed molecular surface definition. 136Using cubic B-spline discretization 137Grid dimension: 33 33 33 138Coarse grid lengths: 13.801 18.154 10.192 139Fine grid lengths: 13.801 18.154 10.192 140Grid spacings: 0.500 0.500 0.500 141Solute dielectric (pdie): 1.000 142Solvent dielectric (sdie): 78.540 143Temperature: 298.150 144Surface sphere density (sdens): 10.000 145Surface tension: 0.105 146radiopt is set to 3 147 148 Number of triangulated 3-point waters found: 0 149 150-------------------------------------------------------------------------------- 151 4. RESULTS 152-------------------------------------------------------------------------------- 153 154iAPBS: unpacked coordinates, charge and radius: 155 1 2.000 1.000 0.000 0.112 1.487 156 2 2.000 2.090 0.000 -0.366 1.908 157 3 1.486 2.454 0.890 0.112 1.487 158 4 1.486 2.454 -0.890 0.112 1.487 159 5 3.427 2.641 0.000 0.597 1.908 160 6 4.391 1.877 0.000 -0.568 1.661 161 7 3.555 3.970 0.000 -0.416 1.824 162 8 2.733 4.556 0.000 0.272 0.600 163 9 4.853 4.614 0.000 0.034 1.908 164 10 5.408 4.316 0.890 0.082 1.387 165 11 5.661 4.221 -1.232 -0.182 1.908 166 12 5.123 4.521 -2.131 0.060 1.487 167 13 6.630 4.719 -1.206 0.060 1.487 168 14 5.809 3.141 -1.241 0.060 1.487 169 15 4.713 6.129 0.000 0.597 1.908 170 16 3.601 6.653 0.000 -0.568 1.661 171 17 5.846 6.835 0.000 -0.416 1.824 172 18 6.737 6.359 0.000 0.272 0.600 173 19 5.846 8.284 0.000 -0.149 1.908 174 20 4.819 8.648 0.000 0.098 1.387 175 21 6.360 8.648 0.890 0.098 1.387 176 22 6.360 8.648 -0.890 0.098 1.387 177iAPBS: Calling apbsdrv 178iAPBS: apbs return code: 0 179iAPBS: apbs return code: 0 180iAPBS: TotalForces: 1 4.108 0.761 -0.017 181iAPBS: TotalForces: 2 6.437 8.400 0.055 182iAPBS: TotalForces: 3 0.126 -1.054 -1.019 183iAPBS: TotalForces: 4 0.162 -1.035 0.979 184iAPBS: TotalForces: 5 -10.816 -5.205 3.291 185iAPBS: TotalForces: 6 -15.856 -9.593 9.277 186iAPBS: TotalForces: 7 -1.998 -18.943 -5.755 187iAPBS: TotalForces: 8 1.173 1.094 -0.176 188iAPBS: TotalForces: 9 8.610 9.436 1.432 189iAPBS: TotalForces: 10 -0.417 -0.207 1.012 190iAPBS: TotalForces: 11 0.958 -4.145 -7.140 191iAPBS: TotalForces: 12 0.424 -0.661 -1.502 192iAPBS: TotalForces: 13 1.974 -4.806 -3.120 193iAPBS: TotalForces: 14 9.767 6.261 -7.979 194iAPBS: TotalForces: 15 -1.239 0.475 7.502 195iAPBS: TotalForces: 16 -5.177 -1.051 -0.431 196iAPBS: TotalForces: 17 -1.541 8.188 3.810 197iAPBS: TotalForces: 18 -3.350 -2.477 -0.165 198iAPBS: TotalForces: 19 6.599 4.841 -0.004 199iAPBS: TotalForces: 20 0.937 6.805 -0.022 200iAPBS: TotalForces: 21 -0.437 1.472 0.515 201iAPBS: TotalForces: 22 -0.447 1.444 -0.543 202iAPBS: SolventForces: 1 0.000 0.000 0.000 203iAPBS: SolventForces: 2 0.000 0.000 0.000 204iAPBS: SolventForces: 3 0.000 0.000 0.000 205iAPBS: SolventForces: 4 0.000 0.000 0.000 206iAPBS: SolventForces: 5 0.000 0.000 0.000 207iAPBS: SolventForces: 6 0.000 0.000 0.000 208iAPBS: SolventForces: 7 0.000 0.000 0.000 209iAPBS: SolventForces: 8 0.000 0.000 0.000 210iAPBS: SolventForces: 9 0.000 0.000 0.000 211iAPBS: SolventForces: 10 0.000 0.000 0.000 212iAPBS: SolventForces: 11 0.000 0.000 0.000 213iAPBS: SolventForces: 12 0.000 0.000 0.000 214iAPBS: SolventForces: 13 0.000 0.000 0.000 215iAPBS: SolventForces: 14 0.000 0.000 0.000 216iAPBS: SolventForces: 15 0.000 0.000 0.000 217iAPBS: SolventForces: 16 0.000 0.000 0.000 218iAPBS: SolventForces: 17 0.000 0.000 0.000 219iAPBS: SolventForces: 18 0.000 0.000 0.000 220iAPBS: SolventForces: 19 0.000 0.000 0.000 221iAPBS: SolventForces: 20 0.000 0.000 0.000 222iAPBS: SolventForces: 21 0.000 0.000 0.000 223iAPBS: SolventForces: 22 0.000 0.000 0.000 224iAPBS: VacuumForces: 1 0.000 0.000 0.000 225iAPBS: VacuumForces: 2 0.000 0.000 0.000 226iAPBS: VacuumForces: 3 0.000 0.000 0.000 227iAPBS: VacuumForces: 4 0.000 0.000 0.000 228iAPBS: VacuumForces: 5 0.000 0.000 0.000 229iAPBS: VacuumForces: 6 0.000 0.000 0.000 230iAPBS: VacuumForces: 7 0.000 0.000 0.000 231iAPBS: VacuumForces: 8 0.000 0.000 0.000 232iAPBS: VacuumForces: 9 0.000 0.000 0.000 233iAPBS: VacuumForces: 10 0.000 0.000 0.000 234iAPBS: VacuumForces: 11 0.000 0.000 0.000 235iAPBS: VacuumForces: 12 0.000 0.000 0.000 236iAPBS: VacuumForces: 13 0.000 0.000 0.000 237iAPBS: VacuumForces: 14 0.000 0.000 0.000 238iAPBS: VacuumForces: 15 0.000 0.000 0.000 239iAPBS: VacuumForces: 16 0.000 0.000 0.000 240iAPBS: VacuumForces: 17 0.000 0.000 0.000 241iAPBS: VacuumForces: 18 0.000 0.000 0.000 242iAPBS: VacuumForces: 19 0.000 0.000 0.000 243iAPBS: VacuumForces: 20 0.000 0.000 0.000 244iAPBS: VacuumForces: 21 0.000 0.000 0.000 245iAPBS: VacuumForces: 22 0.000 0.000 0.000 246iAPBS: SolvForces: 1 0.000 0.000 0.000 247iAPBS: SolvForces: 2 0.000 0.000 0.000 248iAPBS: SolvForces: 3 0.000 0.000 0.000 249iAPBS: SolvForces: 4 0.000 0.000 0.000 250iAPBS: SolvForces: 5 0.000 0.000 0.000 251iAPBS: SolvForces: 6 0.000 0.000 0.000 252iAPBS: SolvForces: 7 0.000 0.000 0.000 253iAPBS: SolvForces: 8 0.000 0.000 0.000 254iAPBS: SolvForces: 9 0.000 0.000 0.000 255iAPBS: SolvForces: 10 0.000 0.000 0.000 256iAPBS: SolvForces: 11 0.000 0.000 0.000 257iAPBS: SolvForces: 12 0.000 0.000 0.000 258iAPBS: SolvForces: 13 0.000 0.000 0.000 259iAPBS: SolvForces: 14 0.000 0.000 0.000 260iAPBS: SolvForces: 15 0.000 0.000 0.000 261iAPBS: SolvForces: 16 0.000 0.000 0.000 262iAPBS: SolvForces: 17 0.000 0.000 0.000 263iAPBS: SolvForces: 18 0.000 0.000 0.000 264iAPBS: SolvForces: 19 0.000 0.000 0.000 265iAPBS: SolvForces: 20 0.000 0.000 0.000 266iAPBS: SolvForces: 21 0.000 0.000 0.000 267iAPBS: SolvForces: 22 0.000 0.000 0.000 268iAPBS: qfForces: 1 0.000 0.000 0.000 269iAPBS: qfForces: 2 0.000 0.000 0.000 270iAPBS: qfForces: 3 0.000 0.000 0.000 271iAPBS: qfForces: 4 0.000 0.000 0.000 272iAPBS: qfForces: 5 0.000 0.000 0.000 273iAPBS: qfForces: 6 0.000 0.000 0.000 274iAPBS: qfForces: 7 0.000 0.000 0.000 275iAPBS: qfForces: 8 0.000 0.000 0.000 276iAPBS: qfForces: 9 0.000 0.000 0.000 277iAPBS: qfForces: 10 0.000 0.000 0.000 278iAPBS: qfForces: 11 0.000 0.000 0.000 279iAPBS: qfForces: 12 0.000 0.000 0.000 280iAPBS: qfForces: 13 0.000 0.000 0.000 281iAPBS: qfForces: 14 0.000 0.000 0.000 282iAPBS: qfForces: 15 0.000 0.000 0.000 283iAPBS: qfForces: 16 0.000 0.000 0.000 284iAPBS: qfForces: 17 0.000 0.000 0.000 285iAPBS: qfForces: 18 0.000 0.000 0.000 286iAPBS: qfForces: 19 0.000 0.000 0.000 287iAPBS: qfForces: 20 0.000 0.000 0.000 288iAPBS: qfForces: 21 0.000 0.000 0.000 289iAPBS: qfForces: 22 0.000 0.000 0.000 290iAPBS: ibForces: 1 0.000 0.000 0.000 291iAPBS: ibForces: 2 0.000 0.000 0.000 292iAPBS: ibForces: 3 0.000 0.000 0.000 293iAPBS: ibForces: 4 0.000 0.000 0.000 294iAPBS: ibForces: 5 0.000 0.000 0.000 295iAPBS: ibForces: 6 0.000 0.000 0.000 296iAPBS: ibForces: 7 0.000 0.000 0.000 297iAPBS: ibForces: 8 0.000 0.000 0.000 298iAPBS: ibForces: 9 0.000 0.000 0.000 299iAPBS: ibForces: 10 0.000 0.000 0.000 300iAPBS: ibForces: 11 0.000 0.000 0.000 301iAPBS: ibForces: 12 0.000 0.000 0.000 302iAPBS: ibForces: 13 0.000 0.000 0.000 303iAPBS: ibForces: 14 0.000 0.000 0.000 304iAPBS: ibForces: 15 0.000 0.000 0.000 305iAPBS: ibForces: 16 0.000 0.000 0.000 306iAPBS: ibForces: 17 0.000 0.000 0.000 307iAPBS: ibForces: 18 0.000 0.000 0.000 308iAPBS: ibForces: 19 0.000 0.000 0.000 309iAPBS: ibForces: 20 0.000 0.000 0.000 310iAPBS: ibForces: 21 0.000 0.000 0.000 311iAPBS: ibForces: 22 0.000 0.000 0.000 312iAPBS: npForces: 1 0.000 0.000 0.000 313iAPBS: npForces: 2 0.000 0.000 0.000 314iAPBS: npForces: 3 0.000 0.000 0.000 315iAPBS: npForces: 4 0.000 0.000 0.000 316iAPBS: npForces: 5 0.000 0.000 0.000 317iAPBS: npForces: 6 0.000 0.000 0.000 318iAPBS: npForces: 7 0.000 0.000 0.000 319iAPBS: npForces: 8 0.000 0.000 0.000 320iAPBS: npForces: 9 0.000 0.000 0.000 321iAPBS: npForces: 10 0.000 0.000 0.000 322iAPBS: npForces: 11 0.000 0.000 0.000 323iAPBS: npForces: 12 0.000 0.000 0.000 324iAPBS: npForces: 13 0.000 0.000 0.000 325iAPBS: npForces: 14 0.000 0.000 0.000 326iAPBS: npForces: 15 0.000 0.000 0.000 327iAPBS: npForces: 16 0.000 0.000 0.000 328iAPBS: npForces: 17 0.000 0.000 0.000 329iAPBS: npForces: 18 0.000 0.000 0.000 330iAPBS: npForces: 19 0.000 0.000 0.000 331iAPBS: npForces: 20 0.000 0.000 0.000 332iAPBS: npForces: 21 0.000 0.000 0.000 333iAPBS: npForces: 22 0.000 0.000 0.000 334iAPBS: dbForces: 1 0.000 0.000 0.000 335iAPBS: dbForces: 2 0.000 0.000 0.000 336iAPBS: dbForces: 3 0.000 0.000 0.000 337iAPBS: dbForces: 4 0.000 0.000 0.000 338iAPBS: dbForces: 5 0.000 0.000 0.000 339iAPBS: dbForces: 6 0.000 0.000 0.000 340iAPBS: dbForces: 7 0.000 0.000 0.000 341iAPBS: dbForces: 8 0.000 0.000 0.000 342iAPBS: dbForces: 9 0.000 0.000 0.000 343iAPBS: dbForces: 10 0.000 0.000 0.000 344iAPBS: dbForces: 11 0.000 0.000 0.000 345iAPBS: dbForces: 12 0.000 0.000 0.000 346iAPBS: dbForces: 13 0.000 0.000 0.000 347iAPBS: dbForces: 14 0.000 0.000 0.000 348iAPBS: dbForces: 15 0.000 0.000 0.000 349iAPBS: dbForces: 16 0.000 0.000 0.000 350iAPBS: dbForces: 17 0.000 0.000 0.000 351iAPBS: dbForces: 18 0.000 0.000 0.000 352iAPBS: dbForces: 19 0.000 0.000 0.000 353iAPBS: dbForces: 20 0.000 0.000 0.000 354iAPBS: dbForces: 21 0.000 0.000 0.000 355iAPBS: dbForces: 22 0.000 0.000 0.000 356 357 358 NSTEP ENERGY RMS GMAX NAME NUMBER 359 1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7 360 361 BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071 362 VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348 363 1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000 364 ENPOLAR = 9.9161 365 366 367 Maximum number of minimization cycles reached. 368 369 370 FINAL RESULTS 371 372 373 374 NSTEP ENERGY RMS GMAX NAME NUMBER 375 1 -1.9290E+01 5.3610E+00 1.8943E+01 N 7 376 377 BOND = 0.0206 ANGLE = 0.3620 DIHED = 8.1071 378 VDWAALS = 2.8120 EEL = -80.1238 EPB = -14.3348 379 1-4 VDW = 5.0157 1-4 EEL = 48.9355 RESTRAINT = 0.0000 380 ENPOLAR = 9.9161 381 382-------------------------------------------------------------------------------- 383 5. TIMINGS 384-------------------------------------------------------------------------------- 385 386| Read coords time 0.00 ( 0.06% of Total) 387| PB Nonbond 0.88 (100.0% of Nonbo) 388| Nonbond force 0.88 (100.0% of Force) 389| Bond/Angle/Dihedral 0.00 ( 0.01% of Force) 390| Force time 0.88 (100.0% of Runmd) 391| Runmd Time 0.88 (99.69% of Total) 392| Other 0.00 ( 0.25% of Total) 393| Total time 0.88 (100.0% of ALL ) 394 395| Highest rstack allocated: 0 396| Highest istack allocated: 0 397| Job began at 22:04:50.491 on 09/24/2007 398| Setup done at 22:04:50.494 on 09/24/2007 399| Run done at 22:04:51.373 on 09/24/2007 400| wallclock() was called 22 times 401