Mon Oct 10 19:33:15 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 Mon Oct 10 2011 at 19:33:15 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2514 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 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: 0.6067216 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 0.6067216 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.528034 assigned positive charge : 370.7028 centred at (gu) : 89.07061 88.22712 91.92006 assigned negative charge : -362.1759 centred at (gu) : 89.14259 88.21980 91.98074 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6204 nv = 96 ne = 84 npr = 50405 no. pairs analyzed = 50405 no. exposed pairs = 3468 no. arc points = 24218 no. surface atoms = 1171 nbur = 1343 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 297 mr = 3033 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2446 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6158641E-09 2.9510172E-09 midg,1,midg; midg,igrid,midg 6.2242074E-09 3.2958214E-09 1,midg,midg; igrid,midg,midg 9.2123802E-09 1.2691859E-09 gauss-seidel spectral radius is 0.9859383 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 19:33:16 rms-change max change #iterations 0.1107124 16.83962 at 10iterations 9.6895676E-03 1.669952 at 20iterations 8.8715408E-04 0.1489754 at 30iterations 9.7272088E-05 1.8244743E-02 at 40iterations 1.4906567E-05 3.3626556E-03 at 50iterations finished qdiffx linear iterations at : 19:33:19 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.4906567E-05 3.3626556E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 19:33:21 4.253u 0.239s 0:05.76 77.7% 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 Mon Oct 10 2011 at 19:33:21 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2514 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 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: 1.820165 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 1.820165 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.528034 assigned positive charge : 370.7028 centred at (gu) : 87.21137 84.68085 95.75958 assigned negative charge : -362.1759 centred at (gu) : 87.42780 84.65945 95.94209 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24218 grid for indexing accessible points = 1.400000 m= 21822 mr = 42739 m= 3125 mr = 15041 m= 174 mr = 1792 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18593 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) : 0.6067216 object centre at (A) : 30.22550 9.891001 59.66000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8685097E-02 7.5787692E-03 midg,1,midg; midg,igrid,midg 1.2580479E-02 7.7063148E-03 1,midg,midg; igrid,midg,midg 2.5070086E-02 2.8599543E-02 gauss-seidel spectral radius is 0.9985034 estimated iterations to convergence 205 setup time was (sec) 0.9400000 now iterating at: 19:33:22 rms-change max change #iterations 3.739287 197.7817 at 10iterations 1.677687 58.29360 at 20iterations 0.7601863 28.47184 at 30iterations 0.3411982 13.28216 at 40iterations 0.1544501 5.545494 at 50iterations 6.9300354E-02 2.579658 at 60iterations 3.1384993E-02 1.093744 at 70iterations 1.4159747E-02 0.4557343 at 80iterations 6.3879844E-03 0.2092671 at 90iterations 2.8928926E-03 9.5577240E-02 at 100iterations 1.3113403E-03 4.3502808E-02 at 110iterations 5.9883593E-04 2.3481369E-02 at 120iterations finished qdiffx linear iterations at : 19:33:31 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 5.9883593E-04 2.3481369E-02 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 19:33:32 9.858u 0.290s 0:10.78 94.0% 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 Mon Oct 10 2011 at 19:33:32 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2514 !!! WARNING: HIR 101 has a net charge of 0.5140 !!! WARNING: HIR 227 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.730247 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): 3.289000 57.16200 ymin,ymax (A): -14.15400 33.93600 zmin,zma (A): 30.32200 88.99800 x,y,z range (A): 53.87300 48.09000 58.67600 scale (grids/A): 2.730247 object centre (A): 30.22550 9.891001 59.66000 number of atom coordinates read : 2514 total number of charged atoms : 2377 net assigned charge : 8.528034 assigned positive charge : 370.7028 centred at (gu) : 85.81694 82.02111 98.63918 assigned negative charge : -362.1759 centred at (gu) : 86.14158 81.98918 98.91313 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24218 grid for indexing accessible points = 1.400000 m= 70967 mr = 105048 m= 24148 mr = 55330 m= 5313 mr = 18570 m= 707 mr = 3799 m= 47 mr = 445 m= 0 mr = 12 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 71686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19013 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) : 1.820165 object centre at (A) : 30.22550 9.891001 59.66000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4739193 -3.4472574E-02 midg,1,midg; midg,igrid,midg 0.1688989 8.8898912E-02 1,midg,midg; igrid,midg,midg 0.2122078 0.5363348 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 1.660000 now iterating at: 19:33:34 rms-change max change #iterations 9.089307 298.9627 at 10iterations 5.282771 117.6020 at 20iterations 3.054434 76.99168 at 30iterations 1.754149 37.38447 at 40iterations 1.006616 20.56907 at 50iterations 0.5746442 11.72539 at 60iterations 0.3281547 7.107616 at 70iterations 0.1869829 3.823347 at 80iterations 0.1062983 2.061970 at 90iterations 6.0427938E-02 1.239051 at 100iterations 3.4330569E-02 0.7219925 at 110iterations 1.9493425E-02 0.3966208 at 120iterations 1.1071730E-02 0.2263913 at 130iterations 6.3066003E-03 0.1270218 at 140iterations 3.5811428E-03 7.1481705E-02 at 150iterations 2.0399960E-03 4.2936325E-02 at 160iterations 1.1609307E-03 2.2858769E-02 at 170iterations 6.6275173E-04 1.3694763E-02 at 180iterations finished qdiffx linear iterations at : 19:33:48 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 6.6275173E-04 1.3694763E-02 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 19:33:50 15.960u 0.341s 0:17.77 91.7% 0+0k 0+0io 0pf+0w