Sat Oct 8 15:01:53 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 Sat Oct 8 2011 at 15:01:54 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 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: 0.6216819 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 0.6216819 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3085 net assigned charge : 4.000006 assigned positive charge : 482.4037 centred at (gu) : 88.71647 88.60114 90.36279 assigned negative charge : -478.4052 centred at (gu) : 88.65849 88.59550 90.38700 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8181 nv = 96 ne = 84 npr = 67011 no. pairs analyzed = 67011 no. exposed pairs = 3644 no. arc points = 25509 no. surface atoms = 1238 nbur = 1992 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 4712 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1155036E-09 1.4868805E-09 midg,1,midg; midg,igrid,midg 4.0138421E-09 2.9333900E-09 1,midg,midg; igrid,midg,midg -2.1202764E-09 6.3534533E-09 gauss-seidel spectral radius is 0.9866496 estimated iterations to convergence 71 setup time was (sec) 0.7200000 now iterating at: 15:01:55 rms-change max change #iterations 0.1475124 19.33113 at 10iterations 1.3899129E-02 1.822556 at 20iterations 1.3813284E-03 0.1849346 at 30iterations 1.5417744E-04 1.8486023E-02 at 40iterations 2.2939192E-05 3.0021667E-03 at 50iterations finished qdiffx linear iterations at : 15:01:59 total time elapsed so far: 5.130000 # loops : 50 mean,max change (kT/e) : 2.2939192E-05 3.0021667E-03 energy calculations done at 5.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.310000 DelPhi exited at 15:02:00 5.312u 0.466s 0:06.11 94.4% 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 Sat Oct 8 2011 at 15:02:00 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 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: 1.865046 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 1.865046 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3085 net assigned charge : 4.000006 assigned positive charge : 482.4037 centred at (gu) : 86.14864 85.80265 91.08768 assigned negative charge : -478.4052 centred at (gu) : 85.97535 85.78603 91.16084 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 32405 mr = 65172 m= 4584 mr = 24144 m= 232 mr = 2778 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1237 time to turn everything in is 0.7400000 number of dielectric boundary points 35606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 214 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24205 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) : 0.6216819 object centre at (A) : 75.17800 2.033501 27.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2523309E-02 -4.3394198E-03 midg,1,midg; midg,igrid,midg -2.6442548E-03 5.1071756E-03 1,midg,midg; igrid,midg,midg 5.4447807E-04 3.4967337E-02 gauss-seidel spectral radius is 0.9986326 estimated iterations to convergence 214 setup time was (sec) 1.090000 now iterating at: 15:02:01 rms-change max change #iterations 4.565463 164.6738 at 10iterations 2.132139 66.26549 at 20iterations 1.002320 31.01142 at 30iterations 0.4691899 14.00520 at 40iterations 0.2201972 6.575738 at 50iterations 0.1031360 2.964475 at 60iterations 4.8339713E-02 1.339985 at 70iterations 2.2738591E-02 0.6416492 at 80iterations 1.0659918E-02 0.2923594 at 90iterations 5.0070714E-03 0.1509819 at 100iterations 2.3437450E-03 6.5376282E-02 at 110iterations 1.1077928E-03 3.0060768E-02 at 120iterations finished qdiffx linear iterations at : 15:02:13 total time elapsed so far: 12.50000 # loops : 120 mean,max change (kT/e) : 1.1077928E-03 3.0060768E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 15:02:13 12.685u 0.530s 0:13.50 97.8% 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 Sat Oct 8 2011 at 15:02:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3230 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: 2.797569 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): 46.54600 103.8100 ymin,ymax (A): -24.70000 28.76700 zmin,zma (A): 2.240000 53.18200 x,y,z range (A): 57.26401 53.46700 50.94200 scale (grids/A): 2.797569 object centre (A): 75.17800 2.033501 27.71100 number of atom coordinates read : 3230 total number of charged atoms : 3085 net assigned charge : 4.000006 assigned positive charge : 482.4037 centred at (gu) : 84.22276 83.70380 91.63113 assigned negative charge : -478.4052 centred at (gu) : 83.96282 83.67902 91.74100 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 209978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 106990 mr = 157772 m= 36554 mr = 88611 m= 7941 mr = 29193 m= 946 mr = 5801 m= 41 mr = 576 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3989 time to turn everything in is 1.970000 number of dielectric boundary points 80488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 24679 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) : 1.865046 object centre at (A) : 75.17800 2.033501 27.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2081425 -9.1858231E-02 midg,1,midg; midg,igrid,midg -0.2474724 3.1890996E-02 1,midg,midg; igrid,midg,midg 4.0913537E-02 0.3766311 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.360000 now iterating at: 15:02:16 rms-change max change #iterations 10.67248 357.0501 at 10iterations 6.210312 123.5440 at 20iterations 3.602566 71.00302 at 30iterations 2.080903 36.49860 at 40iterations 1.200716 22.46950 at 50iterations 0.6944851 11.57035 at 60iterations 0.4004323 7.274767 at 70iterations 0.2312281 3.592126 at 80iterations 0.1331068 2.107171 at 90iterations 7.6640815E-02 1.259519 at 100iterations 4.4185460E-02 0.7741470 at 110iterations 2.5473576E-02 0.4648242 at 120iterations 1.4708846E-02 0.2557168 at 130iterations 8.4875189E-03 0.1385593 at 140iterations 4.9235891E-03 8.3335876E-02 at 150iterations 2.8548869E-03 4.7544479E-02 at 160iterations 1.6698535E-03 2.9018402E-02 at 170iterations 9.8412193E-04 1.7240524E-02 at 180iterations finished qdiffx linear iterations at : 15:02:35 total time elapsed so far: 21.71000 # loops : 180 mean,max change (kT/e) : 9.8412193E-04 1.7240524E-02 energy calculations done at 21.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.88000 DelPhi exited at 15:02:36 21.888u 0.559s 0:22.82 98.2% 0+0k 0+0io 0pf+0w