Sun Oct 9 11:49:41 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 Sun Oct 9 2011 at 11:49:41 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 !!! WARNING: HIR 203 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: 0.6543155 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 0.6543155 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.514009 assigned positive charge : 396.5791 centred at (gu) : 90.56437 90.13118 91.28520 assigned negative charge : -394.0667 centred at (gu) : 90.63560 90.11662 91.21471 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8106 nv = 96 ne = 84 npr = 50488 no. pairs analyzed = 50488 no. exposed pairs = 3767 no. arc points = 26852 no. surface atoms = 1254 nbur = 1395 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 496 mr = 4051 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2568 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9421 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2128368E-09 2.2961318E-08 midg,1,midg; midg,igrid,midg 2.7727030E-09 8.1014644E-09 1,midg,midg; igrid,midg,midg 1.5646293E-08 -8.0158529E-09 gauss-seidel spectral radius is 0.9879226 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 11:49:41 rms-change max change #iterations 0.1603475 26.67374 at 10iterations 1.6581330E-02 2.087387 at 20iterations 1.7166724E-03 0.2206535 at 30iterations 1.7798282E-04 2.6916027E-02 at 40iterations 1.9347259E-05 2.6314259E-03 at 50iterations finished qdiffx linear iterations at : 11:49:45 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.9347259E-05 2.6314259E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 11:49:45 4.085u 0.254s 0:04.60 94.1% 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 11:49:45 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 !!! WARNING: HIR 203 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: 1.962947 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 1.962947 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.514009 assigned positive charge : 396.5791 centred at (gu) : 91.69214 90.39276 93.85465 assigned negative charge : -394.0667 centred at (gu) : 91.90646 90.34976 93.64381 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26852 grid for indexing accessible points = 1.400000 m= 31946 mr = 56898 m= 6213 mr = 22525 m= 500 mr = 3911 m= 4 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 598 time to turn everything in is 0.7700000 number of dielectric boundary points 41209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20331 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) : 0.6543155 object centre at (A) : 21.41550 34.19950 32.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0664661E-03 2.9511672E-02 midg,1,midg; midg,igrid,midg 9.0131909E-04 2.4448339E-02 1,midg,midg; igrid,midg,midg -1.2547179E-03 -3.8203953E-03 gauss-seidel spectral radius is 0.9987504 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 11:49:47 rms-change max change #iterations 4.563054 182.4648 at 10iterations 2.208002 75.49783 at 20iterations 1.062104 31.58232 at 30iterations 0.5144823 14.89518 at 40iterations 0.2483308 7.021530 at 50iterations 0.1198175 3.737740 at 60iterations 5.8069482E-02 1.783641 at 70iterations 2.8018070E-02 0.9172359 at 80iterations 1.3592201E-02 0.3920002 at 90iterations 6.5728677E-03 0.2166758 at 100iterations 3.1738649E-03 9.7202301E-02 at 110iterations 1.5386457E-03 4.7988892E-02 at 120iterations finished qdiffx linear iterations at : 11:49:55 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.5386457E-03 4.7988892E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 11:49:56 9.667u 0.295s 0:10.26 96.9% 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 11:49:56 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2649 !!! WARNING: HIR 203 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: 2.944420 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): -4.835000 47.66600 ymin,ymax (A): 8.686001 59.71300 zmin,zma (A): 5.271000 59.67900 x,y,z range (A): 52.50100 51.02700 54.40800 scale (grids/A): 2.944420 object centre (A): 21.41550 34.19950 32.47500 number of atom coordinates read : 2649 total number of charged atoms : 2571 net assigned charge : 2.514009 assigned positive charge : 396.5791 centred at (gu) : 92.53817 90.58909 95.78167 assigned negative charge : -394.0667 centred at (gu) : 92.85970 90.52466 95.46581 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 198669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26852 grid for indexing accessible points = 1.400000 m= 99720 mr = 138550 m= 39735 mr = 79029 m= 11535 mr = 31224 m= 2174 mr = 8550 m= 177 mr = 1526 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 2040 time to turn everything in is 2.020000 number of dielectric boundary points 93054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 20568 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) : 1.962947 object centre at (A) : 21.41550 34.19950 32.47500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5229394E-02 0.3790163 midg,1,midg; midg,igrid,midg 3.5208572E-02 0.2519272 1,midg,midg; igrid,midg,midg -9.2597008E-02 0.2215582 gauss-seidel spectral radius is 0.9993170 estimated iterations to convergence 302 setup time was (sec) 2.350000 now iterating at: 11:49:58 rms-change max change #iterations 10.85573 558.5157 at 10iterations 6.595556 162.9979 at 20iterations 3.982799 87.45024 at 30iterations 2.396406 50.68306 at 40iterations 1.432713 30.71553 at 50iterations 0.8548713 24.01964 at 60iterations 0.5073792 9.491536 at 70iterations 0.3015051 5.854950 at 80iterations 0.1784725 3.119871 at 90iterations 0.1052467 1.846497 at 100iterations 6.2078696E-02 1.169847 at 110iterations 3.6663879E-02 0.7240463 at 120iterations 2.1618007E-02 0.3741210 at 130iterations 1.2727460E-02 0.2325020 at 140iterations 7.4943523E-03 0.1370010 at 150iterations 4.4188509E-03 7.5340271E-02 at 160iterations 2.6000859E-03 4.7375917E-02 at 170iterations 1.5332921E-03 2.5985003E-02 at 180iterations finished qdiffx linear iterations at : 11:50:12 total time elapsed so far: 16.49000 # loops : 180 mean,max change (kT/e) : 1.5332921E-03 2.5985003E-02 energy calculations done at 16.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.67000 DelPhi exited at 11:50:13 16.670u 0.314s 0:17.27 98.3% 0+0k 0+0io 0pf+0w