Sat Oct 15 15:05:42 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 Sat Oct 15 2011 at 15:05:42 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 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: 0.5483587 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 0.5483587 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3268 net assigned charge : -7.910981 assigned positive charge : 515.2663 centred at (gu) : 87.84811 91.54546 88.10638 assigned negative charge : -523.1788 centred at (gu) : 87.80119 91.53156 88.11663 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6532 nv = 96 ne = 84 npr = 69633 no. pairs analyzed = 69633 no. exposed pairs = 4389 no. arc points = 30811 no. surface atoms = 1475 nbur = 1940 mkacc time = 0.1200000 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 = 1.568000 m= 273 mr = 3295 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2500000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3137 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9410239E-10 -3.9131795E-10 midg,1,midg; midg,igrid,midg -4.4582066E-10 -5.9276600E-10 1,midg,midg; igrid,midg,midg -1.5749785E-09 -8.6793038E-11 gauss-seidel spectral radius is 0.9828843 estimated iterations to convergence 63 setup time was (sec) 0.4600000 now iterating at: 15:05:43 rms-change max change #iterations 8.1602432E-02 14.23564 at 10iterations 5.9277853E-03 0.9889660 at 20iterations 6.0389168E-04 9.8201752E-02 at 30iterations 1.2648788E-04 2.4246216E-02 at 40iterations 3.2979104E-05 6.4201355E-03 at 50iterations finished qdiffx linear iterations at : 15:05:46 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 3.2979104E-05 6.4201355E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 15:05:47 3.690u 0.189s 0:04.36 88.7% 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 Sat Oct 15 2011 at 15:05:47 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 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: 1.645076 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 1.645076 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3268 net assigned charge : -7.910981 assigned positive charge : 515.2663 centred at (gu) : 83.54339 94.63582 84.31828 assigned negative charge : -523.1788 centred at (gu) : 83.40333 94.59441 84.34931 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22854 mr = 47621 m= 2551 mr = 15708 m= 68 mr = 1276 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2138 time to turn everything in is 0.3700000 number of dielectric boundary points 32483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 25155 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) : 0.5483587 object centre at (A) : 37.04450 63.29150 52.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9704973E-03 -1.9377235E-03 midg,1,midg; midg,igrid,midg -4.5857793E-03 6.8645021E-03 1,midg,midg; igrid,midg,midg -2.0878943E-02 2.9484782E-02 gauss-seidel spectral radius is 0.9982480 estimated iterations to convergence 190 setup time was (sec) 0.6200000 now iterating at: 15:05:48 rms-change max change #iterations 3.672294 167.9873 at 10iterations 1.545058 60.69974 at 20iterations 0.6545315 25.02414 at 30iterations 0.2760358 10.68726 at 40iterations 0.1167650 3.922319 at 50iterations 4.9576558E-02 1.785334 at 60iterations 2.1067336E-02 0.7092857 at 70iterations 8.9499811E-03 0.3800621 at 80iterations 3.8333491E-03 0.1500659 at 90iterations 1.6610969E-03 5.4735184E-02 at 100iterations 7.4094615E-04 3.1097412E-02 at 110iterations 3.4464660E-04 1.5014648E-02 at 120iterations finished qdiffx linear iterations at : 15:05:55 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 3.4464660E-04 1.5014648E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 15:05:56 8.350u 0.230s 0:08.92 96.1% 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 Sat Oct 15 2011 at 15:05:56 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 295 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: 2.467614 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): 4.584000 69.50500 ymin,ymax (A): 32.27000 94.31300 zmin,zma (A): 24.80300 79.50200 x,y,z range (A): 64.92101 62.04300 54.69900 scale (grids/A): 2.467614 object centre (A): 37.04450 63.29150 52.15250 number of atom coordinates read : 3415 total number of charged atoms : 3268 net assigned charge : -7.910981 assigned positive charge : 515.2663 centred at (gu) : 80.31471 96.95351 81.47729 assigned negative charge : -523.1788 centred at (gu) : 80.10471 96.89155 81.52381 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77398 mr = 116781 m= 23183 mr = 60854 m= 4041 mr = 17447 m= 248 mr = 2593 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 7423 time to turn everything in is 0.9100000 number of dielectric boundary points 73274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26109 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) : 1.645076 object centre at (A) : 37.04450 63.29150 52.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1255126 -4.3304849E-02 midg,1,midg; midg,igrid,midg 4.9425032E-02 0.1518281 1,midg,midg; igrid,midg,midg -0.5223526 0.5964375 gauss-seidel spectral radius is 0.9991682 estimated iterations to convergence 274 setup time was (sec) 1.190000 now iterating at: 15:05:57 rms-change max change #iterations 9.465403 291.5420 at 10iterations 5.382095 134.3707 at 20iterations 3.047688 76.74879 at 30iterations 1.713078 40.88725 at 40iterations 0.9618008 23.03440 at 50iterations 0.5395209 13.08013 at 60iterations 0.3012508 6.570047 at 70iterations 0.1683558 4.437286 at 80iterations 9.3767427E-02 1.964018 at 90iterations 5.2205697E-02 1.150347 at 100iterations 2.9151633E-02 0.6530011 at 110iterations 1.6265642E-02 0.3259888 at 120iterations 9.0661906E-03 0.1769894 at 130iterations 5.0492971E-03 9.8796844E-02 at 140iterations 2.8296190E-03 5.3710938E-02 at 150iterations 1.5918070E-03 3.7879914E-02 at 160iterations 9.0457860E-04 1.9443989E-02 at 170iterations 5.2128430E-04 1.1032104E-02 at 180iterations finished qdiffx linear iterations at : 15:06:10 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 5.2128430E-04 1.1032104E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 15:06:10 13.613u 0.239s 0:14.29 96.8% 0+0k 0+0io 0pf+0w