___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Nov 15 2007 at 14:05:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 ! amber charges, based on kollman, weiner et al ! j. comp chem, vol 7, p 230 (1986) # of charge parameter records: 975 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: ACE 231 has a net charge of -0.0260 !!! WARNING: LYS 263 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5178710 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -60.40600 -10.29000 ymin,ymax (A): -15.98600 52.75700 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 50.11600 68.74300 41.55100 scale (grids/A): 0.5178710 object centre (A): -35.34800 18.38550 6.187500 number of atom coordinates read : 2817 total number of charged atoms : 2713 net assigned charge : 3.974021 assigned positive charge : 404.5115 centred at (gu) : 91.34156 90.93590 90.52030 assigned negative charge : -400.5386 centred at (gu) : 91.20987 90.58476 90.39761 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4748 nv = 96 ne = 84 npr = 59261 no. pairs analyzed = 59261 no. exposed pairs = 3865 no. arc points = 26393 no. surface atoms = 1314 nbur = 1503 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 185 mr = 2111 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2609 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6821960E-09 1.1562474E-08 midg,1,midg; midg,igrid,midg -1.6678182E-08 2.9653666E-08 1,midg,midg; igrid,midg,midg -4.3201234E-09 1.4632050E-08 gauss-seidel spectral radius is 0.9865981 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 14:05:09 rms-change max change #iterations 7.8802221E-02 13.96943 at 10iterations 7.4113733E-03 1.496193 at 20iterations 7.3382683E-04 0.1583366 at 30iterations 8.5221349E-05 1.9355774E-02 at 40iterations 1.2399810E-05 2.8839111E-03 at 50iterations finished qdiffx linear iterations at : 14:05:12 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.2399810E-05 2.8839111E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 14:05:13 3.913u 0.332s 0:04.84 87.6% 0+0k 2344+45920io 4pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Nov 15 2007 at 14:05:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 ! amber charges, based on kollman, weiner et al ! j. comp chem, vol 7, p 230 (1986) # of charge parameter records: 975 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: ACE 231 has a net charge of -0.0260 !!! WARNING: LYS 263 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.553613 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -60.40600 -10.29000 ymin,ymax (A): -15.98600 52.75700 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 50.11600 68.74300 41.55100 scale (grids/A): 1.553613 object centre (A): -35.34800 18.38550 6.187500 number of atom coordinates read : 2817 total number of charged atoms : 2713 net assigned charge : 3.974021 assigned positive charge : 404.5115 centred at (gu) : 94.02410 92.80646 91.56026 assigned negative charge : -400.5386 centred at (gu) : 93.62933 91.75407 91.19267 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 53362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26393 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 14076 mr = 33516 m= 1205 mr = 8482 m= 27 mr = 436 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 26234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20596 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5178710 object centre at (A) : -35.34800 18.38550 6.187500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7928498E-04 1.0847528E-02 midg,1,midg; midg,igrid,midg -3.7354250E-02 6.5173887E-02 1,midg,midg; igrid,midg,midg -5.1201368E-03 2.0810328E-03 gauss-seidel spectral radius is 0.9984720 estimated iterations to convergence 203 setup time was (sec) 0.8300000 now iterating at: 14:05:14 rms-change max change #iterations 3.238402 164.0908 at 10iterations 1.441514 64.72636 at 20iterations 0.6468724 27.37206 at 30iterations 0.2880428 11.98530 at 40iterations 0.1287987 5.528945 at 50iterations 5.7542983E-02 2.319155 at 60iterations 2.5865652E-02 1.156631 at 70iterations 1.1548231E-02 0.4896237 at 80iterations 5.1753707E-03 0.2244546 at 90iterations 2.3281828E-03 9.5346451E-02 at 100iterations 1.0507514E-03 4.4685364E-02 at 110iterations 4.7452506E-04 2.0835876E-02 at 120iterations finished qdiffx linear iterations at : 14:05:22 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 4.7452506E-04 2.0835876E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 14:05:23 8.786u 0.394s 0:09.88 92.8% 0+0k 45456+45272io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Thu Nov 15 2007 at 14:05:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 17 atomic charges read from file fort.12 ! amber charges, based on kollman, weiner et al ! j. comp chem, vol 7, p 230 (1986) # of charge parameter records: 975 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: ACE 231 has a net charge of -0.0260 !!! WARNING: LYS 263 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.330419 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -60.40600 -10.29000 ymin,ymax (A): -15.98600 52.75700 zmin,zma (A): -14.58800 26.96300 x,y,z range (A): 50.11600 68.74300 41.55100 scale (grids/A): 2.330419 object centre (A): -35.34800 18.38550 6.187500 number of atom coordinates read : 2817 total number of charged atoms : 2713 net assigned charge : 3.974021 assigned positive charge : 404.5115 centred at (gu) : 96.03614 94.20965 92.34022 assigned negative charge : -400.5386 centred at (gu) : 95.44406 92.63107 91.78896 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 124160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26393 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 49912 mr = 83396 m= 12492 mr = 36225 m= 1676 mr = 8495 m= 101 mr = 923 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 59267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 21663 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.553613 object centre at (A) : -35.34800 18.38550 6.187500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6484840E-03 7.9913147E-02 midg,1,midg; midg,igrid,midg -0.5039264 0.8662060 1,midg,midg; igrid,midg,midg -3.8227066E-02 -2.5290987E-03 gauss-seidel spectral radius is 0.9991960 estimated iterations to convergence 278 setup time was (sec) 1.630000 now iterating at: 14:05:25 rms-change max change #iterations 8.010180 260.1229 at 10iterations 4.572014 130.9770 at 20iterations 2.583719 69.18896 at 30iterations 1.461134 37.12612 at 40iterations 0.8221030 23.23575 at 50iterations 0.4621166 11.67120 at 60iterations 0.2595822 6.093666 at 70iterations 0.1456911 3.471455 at 80iterations 8.1626587E-02 1.941105 at 90iterations 4.5749597E-02 1.094416 at 100iterations 2.5683887E-02 0.6354465 at 110iterations 1.4353634E-02 0.3244419 at 120iterations 8.0377096E-03 0.1778145 at 130iterations 4.5049610E-03 0.1026230 at 140iterations 2.5285848E-03 5.8393478E-02 at 150iterations 1.4225851E-03 3.2592773E-02 at 160iterations 8.0333860E-04 1.9287109E-02 at 170iterations 4.5602399E-04 1.1600494E-02 at 180iterations finished qdiffx linear iterations at : 14:05:38 total time elapsed so far: 14.14000 # loops : 180 mean,max change (kT/e) : 4.5602399E-04 1.1600494E-02 energy calculations done at 14.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 14:05:39 14.306u 0.484s 0:15.59 94.8% 0+0k 44808+45280io 0pf+0w