Mon Oct 10 13:59:43 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+sph2.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 = amb2.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 13:59:43 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 0.5084116 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 0.5084116 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.485951 assigned positive charge : 663.5319 centred at (gu) : 88.67168 89.98434 91.76907 assigned negative charge : -667.0202 centred at (gu) : 88.68928 90.10671 91.82182 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7130 nv = 96 ne = 84 npr = 91544 no. pairs analyzed = 91544 no. exposed pairs = 5095 no. arc points = 34109 no. surface atoms = 1741 nbur = 2648 mkacc time = 0.1500000 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 = 1.680000 m= 258 mr = 3965 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3520 ## 551 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4471277E-11 -2.5583918E-10 midg,1,midg; midg,igrid,midg 2.2203508E-10 -3.1402195E-10 1,midg,midg; igrid,midg,midg -5.0935896E-12 -5.7584892E-11 gauss-seidel spectral radius is 0.9801801 estimated iterations to convergence 59 setup time was (sec) 0.4800000 now iterating at: 13:59:44 rms-change max change #iterations 6.5060541E-02 11.82075 at 10iterations 4.1949004E-03 0.6644773 at 20iterations 7.3338934E-04 0.1028023 at 30iterations 2.3512842E-04 3.5869598E-02 at 40iterations 8.0308739E-05 1.2626648E-02 at 50iterations finished qdiffx linear iterations at : 13:59:47 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 8.0308739E-05 1.2626648E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 13:59:47 3.556u 0.246s 0:04.23 89.5% 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 13:59:48 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 1.525235 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 1.525235 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.485951 assigned positive charge : 663.5319 centred at (gu) : 86.01408 89.95216 95.30595 assigned negative charge : -667.0202 centred at (gu) : 86.06719 90.31963 95.46512 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24441 mr = 58169 m= 2119 mr = 16973 m= 36 mr = 936 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.4100000 number of dielectric boundary points 31819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31887 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) : 0.5084116 object centre at (A) : 30.55750 13.21300 10.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9734375E-03 -1.3111115E-02 midg,1,midg; midg,igrid,midg 3.3447684E-03 -1.0405935E-02 1,midg,midg; igrid,midg,midg 6.8811085E-03 1.1987726E-02 gauss-seidel spectral radius is 0.9980365 estimated iterations to convergence 179 setup time was (sec) 0.6500000 now iterating at: 13:59:49 rms-change max change #iterations 3.588933 143.3629 at 10iterations 1.441733 49.00761 at 20iterations 0.5814127 20.34758 at 30iterations 0.2348979 7.453835 at 40iterations 9.4970033E-02 3.078431 at 50iterations 3.8512737E-02 1.376495 at 60iterations 1.5632939E-02 0.5970602 at 70iterations 6.4309109E-03 0.2150726 at 80iterations 2.7178912E-03 9.0909958E-02 at 90iterations 1.2163993E-03 4.2739868E-02 at 100iterations 6.0526142E-04 2.3109436E-02 at 110iterations 3.3967011E-04 1.1723518E-02 at 120iterations finished qdiffx linear iterations at : 13:59:57 total time elapsed so far: 8.470000 # loops : 120 mean,max change (kT/e) : 3.3967011E-04 1.1723518E-02 energy calculations done at 8.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 13:59:58 8.604u 0.273s 0:10.07 88.0% 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 13:59:58 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4389 !!! WARNING: HIT 442 has a net charge of 0.5140 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: 2.287852 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): -3.265000 64.38000 ymin,ymax (A): -12.29600 38.72200 zmin,zma (A): -24.55700 45.46500 x,y,z range (A): 67.64500 51.01800 70.02200 scale (grids/A): 2.287852 object centre (A): 30.55750 13.21300 10.45400 number of atom coordinates read : 4389 total number of charged atoms : 4235 net assigned charge : -3.485951 assigned positive charge : 663.5319 centred at (gu) : 84.02100 89.92780 97.95872 assigned negative charge : -667.0202 centred at (gu) : 84.10067 90.47931 98.19750 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 189892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87869 mr = 142549 m= 22812 mr = 70548 m= 3124 mr = 16953 m= 134 mr = 1969 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 272 time to turn everything in is 0.9900000 number of dielectric boundary points 71785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 33767 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) : 1.525235 object centre at (A) : 30.55750 13.21300 10.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1778588 -0.3115026 midg,1,midg; midg,igrid,midg 3.2041084E-02 -0.1707915 1,midg,midg; igrid,midg,midg 0.2228787 0.2974194 gauss-seidel spectral radius is 0.9991177 estimated iterations to convergence 266 setup time was (sec) 1.260000 now iterating at: 14:00:00 rms-change max change #iterations 9.701402 259.9786 at 10iterations 5.440202 119.1684 at 20iterations 3.028141 65.57285 at 30iterations 1.677127 39.51736 at 40iterations 0.9256131 17.86816 at 50iterations 0.5102370 10.53431 at 60iterations 0.2800954 5.430626 at 70iterations 0.1540177 2.906326 at 80iterations 8.4317788E-02 1.564989 at 90iterations 4.6193130E-02 0.9607315 at 100iterations 2.5318956E-02 0.5015597 at 110iterations 1.3882752E-02 0.2670078 at 120iterations 7.6487265E-03 0.1618500 at 130iterations 4.2501041E-03 8.2781434E-02 at 140iterations 2.3812172E-03 4.7396660E-02 at 150iterations 1.3663126E-03 2.6586056E-02 at 160iterations 8.1202795E-04 1.8630981E-02 at 170iterations 5.0854631E-04 1.1128902E-02 at 180iterations finished qdiffx linear iterations at : 14:00:11 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 5.0854631E-04 1.1128902E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 14:00:12 12.832u 0.296s 0:13.80 95.0% 0+0k 0+0io 0pf+0w