Sun Oct 9 11:52:59 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 Sun Oct 9 2011 at 11:53:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1884 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: 0.7364502 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 0.7364502 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 273.6861 centred at (gu) : 89.32462 90.71793 89.98582 assigned negative charge : -271.6865 centred at (gu) : 89.07671 90.64036 90.00263 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7609 nv = 96 ne = 84 npr = 36310 no. pairs analyzed = 36310 no. exposed pairs = 2664 no. arc points = 18760 no. surface atoms = 910 nbur = 974 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 660 mr = 4084 m= 3 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7490772E-08 2.0367715E-08 midg,1,midg; midg,igrid,midg -2.4762082E-08 1.0954025E-07 1,midg,midg; igrid,midg,midg -1.9359338E-07 2.0042471E-07 gauss-seidel spectral radius is 0.9903855 estimated iterations to convergence 83 setup time was (sec) 0.4700000 now iterating at: 11:53:00 rms-change max change #iterations 0.2216680 28.88793 at 10iterations 2.8997673E-02 4.005291 at 20iterations 3.8613253E-03 0.4730453 at 30iterations 5.1237969E-04 6.6398621E-02 at 40iterations 6.9326263E-05 9.2186928E-03 at 50iterations finished qdiffx linear iterations at : 11:53:03 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 6.9326263E-05 9.2186928E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 11:53:03 3.089u 0.126s 0:03.51 91.1% 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 Sun Oct 9 2011 at 11:53:03 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 = 1884 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.209351 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 2.209351 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 273.6861 centred at (gu) : 87.97373 92.15382 89.95786 assigned negative charge : -271.6865 centred at (gu) : 87.23043 91.92136 90.00804 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18760 grid for indexing accessible points = 1.400000 m= 34038 mr = 52541 m= 9266 mr = 25844 m= 1306 mr = 6819 m= 60 mr = 797 m= 0 mr = 19 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 36838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14410 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) : 0.7364502 object centre at (A) : 32.35300 4.712500 113.3895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7991678E-02 2.7993282E-02 midg,1,midg; midg,igrid,midg -1.4169976E-02 1.8413946E-02 1,midg,midg; igrid,midg,midg -4.4082925E-02 4.5391161E-02 gauss-seidel spectral radius is 0.9989178 estimated iterations to convergence 240 setup time was (sec) 0.9000000 now iterating at: 11:53:04 rms-change max change #iterations 4.669453 214.9242 at 10iterations 2.365126 81.25922 at 20iterations 1.197528 37.20907 at 30iterations 0.6091248 18.92657 at 40iterations 0.3098636 9.243431 at 50iterations 0.1573174 4.362951 at 60iterations 8.0100939E-02 2.543562 at 70iterations 4.0652823E-02 1.261711 at 80iterations 2.0658268E-02 0.6071119 at 90iterations 1.0514926E-02 0.3290672 at 100iterations 5.3485977E-03 0.1533575 at 110iterations 2.7257013E-03 8.4263086E-02 at 120iterations finished qdiffx linear iterations at : 11:53:11 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.7257013E-03 8.4263086E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 11:53:12 8.003u 0.253s 0:08.57 96.2% 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 Sun Oct 9 2011 at 11:53:12 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 = 1884 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: 3.314026 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): 8.183001 56.52300 ymin,ymax (A): -19.38100 28.80600 zmin,zma (A): 94.24400 132.5350 x,y,z range (A): 48.34000 48.18700 38.29099 scale (grids/A): 3.314026 object centre (A): 32.35300 4.712500 113.3895 number of atom coordinates read : 1884 total number of charged atoms : 1808 net assigned charge : 2.000006 assigned positive charge : 273.6861 centred at (gu) : 86.96066 93.23085 89.93677 assigned negative charge : -271.6865 centred at (gu) : 85.84570 92.88219 90.01212 start vw surface at 0.1300000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 179270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18760 grid for indexing accessible points = 1.400000 m= 99049 mr = 126434 m= 48828 mr = 81438 m= 18673 mr = 40947 m= 5099 mr = 15395 m= 821 mr = 4068 m= 48 mr = 607 m= 0 mr = 23 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 82876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 14463 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) : 2.209351 object centre at (A) : 32.35300 4.712500 113.3895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4474693 0.2840745 midg,1,midg; midg,igrid,midg -0.1993617 0.6477377 1,midg,midg; igrid,midg,midg -0.2424776 0.3856795 gauss-seidel spectral radius is 0.9993361 estimated iterations to convergence 306 setup time was (sec) 2.220000 now iterating at: 11:53:14 rms-change max change #iterations 10.23008 323.5718 at 10iterations 6.143003 143.1051 at 20iterations 3.679927 82.77876 at 30iterations 2.198359 44.95871 at 40iterations 1.314936 27.06963 at 50iterations 0.7844764 13.83084 at 60iterations 0.4673165 9.482132 at 70iterations 0.2780116 5.063859 at 80iterations 0.1649990 3.278612 at 90iterations 9.8045282E-02 1.636083 at 100iterations 5.8073435E-02 0.9423504 at 110iterations 3.4487899E-02 0.5691664 at 120iterations 2.0434311E-02 0.3297539 at 130iterations 1.2122234E-02 0.2005768 at 140iterations 7.1840878E-03 0.1219704 at 150iterations 4.2548403E-03 7.0732117E-02 at 160iterations 2.5216292E-03 4.1297913E-02 at 170iterations 1.4951171E-03 2.4069786E-02 at 180iterations finished qdiffx linear iterations at : 11:53:28 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 1.4951171E-03 2.4069786E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 11:53:28 15.910u 0.284s 0:16.47 98.2% 0+0k 0+0io 0pf+0w