Tue Oct 11 08:32:47 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 Tue Oct 11 2011 at 08:32:47 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7009806 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 0.7009806 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 88.49346 90.04527 90.88193 assigned negative charge : -306.8872 centred at (gu) : 88.42920 90.21307 90.91322 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6532 nv = 96 ne = 84 npr = 43592 no. pairs analyzed = 43592 no. exposed pairs = 2346 no. arc points = 16158 no. surface atoms = 799 nbur = 1274 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3755 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 0.2600000 number of dielectric boundary points 3073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1550 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7351201E-08 4.9082370E-08 midg,1,midg; midg,igrid,midg 1.2286131E-07 -1.6943087E-08 1,midg,midg; igrid,midg,midg 3.6256633E-08 6.1096060E-08 gauss-seidel spectral radius is 0.9893845 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 08:32:48 rms-change max change #iterations 0.1899894 29.37009 at 10iterations 2.3148941E-02 3.740440 at 20iterations 2.7934157E-03 0.3690948 at 30iterations 3.3390557E-04 4.6203613E-02 at 40iterations 4.0806350E-05 5.1918030E-03 at 50iterations finished qdiffx linear iterations at : 08:32:52 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 4.0806350E-05 5.1918030E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 08:32:52 4.167u 0.203s 0:04.92 88.6% 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 Tue Oct 11 2011 at 08:32:52 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.102942 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 2.102942 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 85.48067 90.13573 92.64590 assigned negative charge : -306.8872 centred at (gu) : 85.28778 90.63937 92.73966 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16158 grid for indexing accessible points = 1.400000 m= 25808 mr = 50053 m= 4524 mr = 19213 m= 452 mr = 3017 m= 15 mr = 267 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5318 time to turn everything in is 0.6200000 number of dielectric boundary points 28318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15426 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) : 0.7009806 object centre at (A) : 20.62800 -3.680499 7.865999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4644227E-02 4.4214670E-02 midg,1,midg; midg,igrid,midg 4.8868995E-02 2.3708493E-03 1,midg,midg; igrid,midg,midg 2.5864409E-02 1.3590669E-02 gauss-seidel spectral radius is 0.9988007 estimated iterations to convergence 229 setup time was (sec) 0.9500000 now iterating at: 08:32:54 rms-change max change #iterations 4.450170 225.2555 at 10iterations 2.188480 74.10487 at 20iterations 1.074010 36.99184 at 30iterations 0.5283481 18.07395 at 40iterations 0.2591332 7.834309 at 50iterations 0.1275892 4.028564 at 60iterations 6.2632620E-02 1.881512 at 70iterations 3.0749571E-02 0.9440193 at 80iterations 1.5189819E-02 0.4342556 at 90iterations 7.4432818E-03 0.2317348 at 100iterations 3.6667173E-03 0.1042786 at 110iterations 1.8064200E-03 5.6589127E-02 at 120iterations finished qdiffx linear iterations at : 08:33:02 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 1.8064200E-03 5.6589127E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 08:33:03 9.630u 0.262s 0:10.40 95.0% 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 Tue Oct 11 2011 at 08:33:03 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.154413 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 3.154413 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 83.22086 90.20357 93.96887 assigned negative charge : -306.8872 centred at (gu) : 82.93164 90.95911 94.10959 start vw surface at 0.1300000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 162162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16158 grid for indexing accessible points = 1.400000 m= 83151 mr = 120953 m= 31026 mr = 68845 m= 8475 mr = 25205 m= 1770 mr = 6481 m= 282 mr = 1355 m= 20 mr = 225 m= 0 mr = 4 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 17622 time to turn everything in is 1.820000 number of dielectric boundary points 63818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 15560 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) : 2.102942 object centre at (A) : 20.62800 -3.680499 7.865999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4269877 0.4067254 midg,1,midg; midg,igrid,midg 0.4053436 -6.3407407E-03 1,midg,midg; igrid,midg,midg 0.3156440 8.0178656E-02 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 2.160000 now iterating at: 08:33:05 rms-change max change #iterations 10.02150 360.2457 at 10iterations 5.884136 153.8019 at 20iterations 3.442910 80.83500 at 30iterations 2.014906 52.05611 at 40iterations 1.178904 25.09586 at 50iterations 0.6882128 13.49443 at 60iterations 0.4001084 6.938601 at 70iterations 0.2337843 4.793512 at 80iterations 0.1359501 3.113434 at 90iterations 7.9048827E-02 1.450745 at 100iterations 4.5987718E-02 0.8502645 at 110iterations 2.6799457E-02 0.5332336 at 120iterations 1.5615349E-02 0.2630386 at 130iterations 9.1306884E-03 0.1680583 at 140iterations 5.3498843E-03 9.4842911E-02 at 150iterations 3.1533386E-03 5.6183815E-02 at 160iterations 1.8750534E-03 3.9073944E-02 at 170iterations 1.1360643E-03 2.1830559E-02 at 180iterations finished qdiffx linear iterations at : 08:33:19 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 1.1360643E-03 2.1830559E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 08:33:19 15.738u 0.282s 0:16.60 96.4% 0+0k 0+0io 0pf+0w