Mon Oct 10 13:59:07 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________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 Mon Oct 10 2011 at 13:59:07 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: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5885659 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 0.5885659 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9999603 assigned positive charge : 636.3094 centred at (gu) : 90.91002 89.52818 88.48966 assigned negative charge : -637.3125 centred at (gu) : 90.75249 89.66066 88.68700 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9566 nv = 96 ne = 84 npr = 88073 no. pairs analyzed = 88073 no. exposed pairs = 4862 no. arc points = 32881 no. surface atoms = 1649 nbur = 2585 mkacc time = 0.2300000 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 = 1.456000 m= 462 mr = 5607 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 114 time to turn everything in is 0.4800000 number of dielectric boundary points 4384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3487 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0774672E-08 -6.2774594E-09 midg,1,midg; midg,igrid,midg 5.5059712E-09 -5.4762834E-09 1,midg,midg; igrid,midg,midg -5.8174852E-09 7.3617810E-09 gauss-seidel spectral radius is 0.9851905 estimated iterations to convergence 67 setup time was (sec) 0.7700000 now iterating at: 13:59:08 rms-change max change #iterations 0.1275275 20.31165 at 10iterations 1.0913497E-02 1.439522 at 20iterations 1.2126185E-03 0.1702213 at 30iterations 2.5611717E-04 3.5785675E-02 at 40iterations 8.1863815E-05 9.5584393E-03 at 50iterations finished qdiffx linear iterations at : 13:59:12 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 8.1863815E-05 9.5584393E-03 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 13:59:13 4.998u 0.388s 0:05.97 89.9% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 13:59:13 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: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.765698 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 1.765698 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9999603 assigned positive charge : 636.3094 centred at (gu) : 92.72870 88.58308 85.46770 assigned negative charge : -637.3125 centred at (gu) : 92.25716 88.98132 86.06063 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 106047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32881 grid for indexing accessible points = 1.400000 m= 38523 mr = 77369 m= 5503 mr = 28995 m= 268 mr = 3509 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 4310 time to turn everything in is 0.8500000 number of dielectric boundary points 40408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 31797 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) : 0.5885659 object centre at (A) : 5.182000 64.21100 60.88050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6528894E-02 -3.5260659E-02 midg,1,midg; midg,igrid,midg 2.6782842E-02 -2.9910658E-02 1,midg,midg; igrid,midg,midg -2.2999462E-02 4.3514099E-02 gauss-seidel spectral radius is 0.9985647 estimated iterations to convergence 209 setup time was (sec) 1.160000 now iterating at: 13:59:15 rms-change max change #iterations 4.856541 197.5613 at 10iterations 2.221246 63.77866 at 20iterations 1.021520 29.49240 at 30iterations 0.4709518 12.52707 at 40iterations 0.2164520 5.827922 at 50iterations 9.9510290E-02 2.806808 at 60iterations 4.5981906E-02 1.235106 at 70iterations 2.1202469E-02 0.5892246 at 80iterations 9.8327594E-03 0.2494373 at 90iterations 4.5720446E-03 0.1240540 at 100iterations 2.1654959E-03 6.3388824E-02 at 110iterations 1.0507723E-03 2.9850006E-02 at 120iterations finished qdiffx linear iterations at : 13:59:25 total time elapsed so far: 11.79000 # loops : 120 mean,max change (kT/e) : 1.0507723E-03 2.9850006E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 13:59:26 11.954u 0.471s 0:12.72 97.6% 0+0k 0+0io 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 Mon Oct 10 2011 at 13:59:26 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: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.648547 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 2.648547 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9999603 assigned positive charge : 636.3094 centred at (gu) : 94.09287 87.87444 83.20116 assigned negative charge : -637.3125 centred at (gu) : 93.38555 88.47193 84.09077 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 246639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32881 grid for indexing accessible points = 1.400000 m= 127336 mr = 187699 m= 43730 mr = 105997 m= 9767 mr = 35512 m= 1148 mr = 7483 m= 36 mr = 735 m= 0 mr = 2 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 14125 time to turn everything in is 2.220000 number of dielectric boundary points 91228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 32688 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) : 1.765698 object centre at (A) : 5.182000 64.21100 60.88050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.034859 -0.4123771 midg,1,midg; midg,igrid,midg 0.3409654 -0.3524448 1,midg,midg; igrid,midg,midg -0.2149083 0.3310059 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 2.580000 now iterating at: 13:59:29 rms-change max change #iterations 11.80283 316.3850 at 10iterations 6.996614 159.1119 at 20iterations 4.108255 101.8001 at 30iterations 2.400930 46.89397 at 40iterations 1.403145 23.94636 at 50iterations 0.8145311 13.32742 at 60iterations 0.4719320 7.384374 at 70iterations 0.2741298 4.297470 at 80iterations 0.1586675 2.619125 at 90iterations 9.1942497E-02 1.489475 at 100iterations 5.3268448E-02 0.8823528 at 110iterations 3.0812718E-02 0.5075219 at 120iterations 1.7846420E-02 0.3071766 at 130iterations 1.0311046E-02 0.1665602 at 140iterations 6.0131699E-03 8.9221954E-02 at 150iterations 3.5226378E-03 5.8167458E-02 at 160iterations 2.0822843E-03 3.5215378E-02 at 170iterations 1.2554602E-03 2.1240234E-02 at 180iterations finished qdiffx linear iterations at : 13:59:46 total time elapsed so far: 19.87000 # loops : 180 mean,max change (kT/e) : 1.2554602E-03 2.1240234E-02 energy calculations done at 19.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.04000 DelPhi exited at 13:59:47 20.047u 0.473s 0:21.27 96.4% 0+0k 0+0io 0pf+0w