Tue Oct 11 03:39:51 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 Tue Oct 11 2011 at 03:39:51 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 73 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6641915 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 0.6641915 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5140148 assigned positive charge : 416.9908 centred at (gu) : 90.22659 90.27523 91.44156 assigned negative charge : -416.4773 centred at (gu) : 89.92378 90.08924 91.38708 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8079 nv = 96 ne = 84 npr = 55956 no. pairs analyzed = 55956 no. exposed pairs = 3268 no. arc points = 22690 no. surface atoms = 1091 nbur = 1639 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4696 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2186 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7201277E-09 1.8835618E-08 midg,1,midg; midg,igrid,midg -4.1168605E-08 4.6758540E-08 1,midg,midg; igrid,midg,midg -6.9251492E-08 7.3731293E-08 gauss-seidel spectral radius is 0.9882580 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 03:39:51 rms-change max change #iterations 0.1770190 26.65606 at 10iterations 1.9635223E-02 2.733456 at 20iterations 2.1857668E-03 0.3077698 at 30iterations 2.6399922E-04 3.1864166E-02 at 40iterations 4.4794589E-05 5.5122375E-03 at 50iterations finished qdiffx linear iterations at : 03:39:54 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.4794589E-05 5.5122375E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 03:39:55 3.370u 0.206s 0:04.05 88.1% 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 Tue Oct 11 2011 at 03:39:55 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 73 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: 1.992574 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 1.992574 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5140148 assigned positive charge : 416.9908 centred at (gu) : 90.67943 90.82516 94.32392 assigned negative charge : -416.4773 centred at (gu) : 89.77091 90.26744 94.16106 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22690 grid for indexing accessible points = 1.400000 m= 33985 mr = 62297 m= 5659 mr = 25865 m= 378 mr = 3696 m= 6 mr = 170 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 408 time to turn everything in is 0.6200000 number of dielectric boundary points 35031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20398 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) : 0.6641915 object centre at (A) : 12.59850 -2.582500 18.70950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1007146E-02 -8.7708747E-03 midg,1,midg; midg,igrid,midg -3.1737819E-02 3.3686545E-02 1,midg,midg; igrid,midg,midg -1.3211270E-02 8.4929742E-02 gauss-seidel spectral radius is 0.9987583 estimated iterations to convergence 225 setup time was (sec) 0.9000000 now iterating at: 03:39:56 rms-change max change #iterations 4.842981 216.6698 at 10iterations 2.363062 75.66597 at 20iterations 1.145860 40.79827 at 30iterations 0.5562954 16.95696 at 40iterations 0.2717852 7.376469 at 50iterations 0.1318585 3.785524 at 60iterations 6.4004704E-02 1.843629 at 70iterations 3.1132504E-02 0.9500694 at 80iterations 1.5110803E-02 0.4169381 at 90iterations 7.3790164E-03 0.2227974 at 100iterations 3.6012768E-03 0.1070200 at 110iterations 1.7726328E-03 4.8538208E-02 at 120iterations finished qdiffx linear iterations at : 03:40:04 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 1.7726328E-03 4.8538208E-02 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.810000 DelPhi exited at 03:40:05 8.813u 0.227s 0:09.87 91.4% 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 Tue Oct 11 2011 at 03:40:05 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 73 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: 2.988862 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 2.988862 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5140148 assigned positive charge : 416.9908 centred at (gu) : 91.01891 91.23775 96.48567 assigned negative charge : -416.4773 centred at (gu) : 89.65635 90.40115 96.24149 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 200576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22690 grid for indexing accessible points = 1.400000 m= 107795 mr = 149723 m= 41678 mr = 90044 m= 10261 mr = 34195 m= 1639 mr = 7909 m= 152 mr = 1207 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 1431 time to turn everything in is 1.590000 number of dielectric boundary points 78949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 20655 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) : 1.992574 object centre at (A) : 12.59850 -2.582500 18.70950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9492162 0.1534469 midg,1,midg; midg,igrid,midg -0.3371163 0.4078467 1,midg,midg; igrid,midg,midg -0.1590179 0.7136683 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.910000 now iterating at: 03:40:07 rms-change max change #iterations 11.11856 396.8059 at 10iterations 6.556256 146.8080 at 20iterations 3.840477 74.30635 at 30iterations 2.250753 57.13794 at 40iterations 1.319243 24.11346 at 50iterations 0.7697506 13.53273 at 60iterations 0.4493363 7.557606 at 70iterations 0.2624454 4.649971 at 80iterations 0.1529334 2.410477 at 90iterations 8.9164577E-02 1.414425 at 100iterations 5.1994938E-02 0.9032974 at 110iterations 3.0257668E-02 0.5080490 at 120iterations 1.7628521E-02 0.3030968 at 130iterations 1.0292845E-02 0.1731014 at 140iterations 6.0169371E-03 0.1026497 at 150iterations 3.5276625E-03 5.8807373E-02 at 160iterations 2.0847567E-03 3.3912659E-02 at 170iterations 1.2418489E-03 2.1242142E-02 at 180iterations finished qdiffx linear iterations at : 03:40:18 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.2418489E-03 2.1242142E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 03:40:18 12.906u 0.227s 0:13.70 95.7% 0+0k 0+0io 0pf+0w