1 2 ------------------------------------------------------- 3 Amber 10 SANDER 2008 4 ------------------------------------------------------- 5 6| Run on 05/28/2008 at 14:02:46 7 [-O]verwriting output 8 9File Assignments: 10| MDIN: mdin 11| MDOUT: lyn.out 12|INPCRD: ./prmtop-inpcrd/lyn.inpcrd 13| PARM: ./prmtop-inpcrd/lyn.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 iAPBS/sander solvation energies (based on pbsa_radi) 27 &cntrl 28 ntx=1, irest=0, 29 imin=1, maxcyc=0, 30 ntpr=1, ntwr=100000, 31 igb=6, ntb=0, 32 ntc=1, ntf=1, tol=0.000001, 33 ntt=0, temp0=300 34 &end 35 &apbs 36 apbs_debug=0, 37 apbs_print=0, 38 grid=0.5, 0.5, 0.5, 39 calc_type=0, 40 cmeth=1, 41 bcfl=2, 42 srfm=1, 43 chgm=1, 44 pdie=1.0, 45 sdie=80.0, 46 srad = 1.4, 47 radiopt=0, 48 calcforce=0, calcnpenergy=1, 49&end 50 51-------------------------------------------------------------------------------- 52 1. RESOURCE USE: 53-------------------------------------------------------------------------------- 54 55| Flags: 56| New format PARM file being parsed. 57| Version = 1.000 Date = 01/07/05 Time = 17:56:14 58 NATOM = 16 NTYPES = 5 NBONH = 11 MBONA = 4 59 NTHETH = 24 MTHETA = 3 NPHIH = 31 MPHIA = 4 60 NHPARM = 0 NPARM = 0 NNB = 77 NRES = 1 61 NBONA = 4 NTHETA = 3 NPHIA = 4 NUMBND = 5 62 NUMANG = 9 NPTRA = 6 NATYP = 5 NPHB = 0 63 IFBOX = 0 NMXRS = 16 IFCAP = 0 NEXTRA = 0 64 NCOPY = 0 65 66 67| Memory Use Allocated 68| Real 1182 69| Hollerith 99 70| Integer 20687 71| Max Pairs 1 72| nblistReal 0 73| nblist Int 0 74| Total 90 kbytes 75| Duplicated 0 dihedrals 76| Duplicated 0 dihedrals 77 78-------------------------------------------------------------------------------- 79 2. CONTROL DATA FOR THE RUN 80-------------------------------------------------------------------------------- 81 82LYN 83 84General flags: 85 imin = 1, nmropt = 0 86 87Nature and format of input: 88 ntx = 1, irest = 0, ntrx = 1 89 90Nature and format of output: 91 ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 100000 92 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 93 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 94 95Potential function: 96 ntf = 1, ntb = 0, igb = 6, nsnb = 25 97 ipol = 0, gbsa = 0, iesp = 0 98 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 99 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 100 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 101 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 102 alpb = 0 103 scnb = 2.00000, scee = 1.20000 104 105Frozen or restrained atoms: 106 ibelly = 0, ntr = 0 107 108Energy minimization: 109 maxcyc = 0, ncyc = 10, ntmin = 1 110 dx0 = 0.01000, drms = 0.00010 111| INFO: Old style inpcrd file read 112 113 114-------------------------------------------------------------------------------- 115 3. ATOMIC COORDINATES AND VELOCITIES 116-------------------------------------------------------------------------------- 117 118LYN 119 begin time read from input coords = 0.000 ps 120 121iAPBS: Initializing APBS interface 122iAPBS: Using charge/radii definition from prmtop file 123iAPBS: Grid dime not specified, calculating ... 124iAPBS: Requesting dime re-calculation on the fly 125 126 APBS calculation parameters: 127 128Nonlinear traditional PBE 129Multiple Debye-Huckel boundary conditions 130Smoothed molecular surface definition 131Using cubic B-spline discretization 132Grid dimension: 33 33 33 133Coarse grid lengths: 9.794 14.169 10.423 A 134Fine grid lengths: 9.794 14.169 10.423 A 135Grid spacings: 0.500 0.500 0.500 A 136Solute dielectric (pdie): 1.000 137Solvent dielectric (sdie): 80.000 138Temperature: 298.150 K 139Surface sphere density (sdens): 10.000 grid points/A^2 140Surface tension: 0.105 kJ/mol/A 141Using charge/radii information from prmtop file 142 143 Number of triangulated 3-point waters found: 0 144 145-------------------------------------------------------------------------------- 146 4. RESULTS 147-------------------------------------------------------------------------------- 148 149 150 151 NSTEP ENERGY RMS GMAX NAME NUMBER 152 1 -5.8138E+00 1.2397E+01 4.9493E+01 HB1 16 153 154 BOND = 2.7553 ANGLE = 0.0734 DIHED = 0.4000 155 VDWAALS = -0.2408 EEL = 6.4144 EPB = -6.3802 156 1-4 VDW = 1.0466 1-4 EEL = -17.0265 RESTRAINT = 0.0000 157 ENPOLAR = 7.1439 158 159 160 Maximum number of minimization cycles reached. 161 162 163 FINAL RESULTS 164 165 166 167 NSTEP ENERGY RMS GMAX NAME NUMBER 168 1 -5.8138E+00 1.2397E+01 4.9493E+01 HB1 16 169 170 BOND = 2.7553 ANGLE = 0.0734 DIHED = 0.4000 171 VDWAALS = -0.2408 EEL = 6.4144 EPB = -6.3802 172 1-4 VDW = 1.0466 1-4 EEL = -17.0265 RESTRAINT = 0.0000 173 ENPOLAR = 7.1439 174 175-------------------------------------------------------------------------------- 176 5. TIMINGS 177-------------------------------------------------------------------------------- 178 179| Read coords time 0.00 ( 0.07% of Total) 180| PB Nonbond 0.78 (100.0% of Nonbo) 181| Nonbond force 0.78 (100.0% of Force) 182| Bond/Angle/Dihedral 0.00 ( 0.01% of Force) 183| Force time 0.78 (100.0% of Runmd) 184| Runmd Time 0.78 (99.65% of Total) 185| Other 0.00 ( 0.28% of Total) 186| Total time 0.78 (100.0% of ALL ) 187 188| Highest rstack allocated: 0 189| Highest istack allocated: 0 190| Job began at 14:02:46.158 on 05/28/2008 191| Setup done at 14:02:46.160 on 05/28/2008 192| Run done at 14:02:46.937 on 05/28/2008 193| wallclock() was called 22 times 194