Mon Oct 10 14:07:49 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 14:07:50 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.7232685 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 0.7232685 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 284.9172 centred at (gu) : 89.62193 90.43043 90.97357 assigned negative charge : -286.4171 centred at (gu) : 89.47378 90.20304 91.02354 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 40649 no. pairs analyzed = 40649 no. exposed pairs = 2417 no. arc points = 17911 no. surface atoms = 809 nbur = 1133 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 3733 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.2500000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1483 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1366499E-08 -6.0421520E-08 midg,1,midg; midg,igrid,midg -1.5348567E-07 1.3564038E-07 1,midg,midg; igrid,midg,midg -1.2293776E-07 7.0180533E-08 gauss-seidel spectral radius is 0.9900277 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 14:07:50 rms-change max change #iterations 0.2178930 29.88012 at 10iterations 2.7952053E-02 3.507967 at 20iterations 3.6196960E-03 0.5195198 at 30iterations 4.5236992E-04 6.8204805E-02 at 40iterations 5.9012520E-05 8.0718994E-03 at 50iterations finished qdiffx linear iterations at : 14:07:53 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 5.9012520E-05 8.0718994E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:07:54 3.224u 0.184s 0:04.46 76.2% 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 Mon Oct 10 2011 at 14:07:54 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.169806 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 2.169806 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 284.9172 centred at (gu) : 88.86580 91.29144 92.92072 assigned negative charge : -286.4171 centred at (gu) : 88.42139 90.60915 93.07082 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17911 grid for indexing accessible points = 1.400000 m= 27915 mr = 49016 m= 6036 mr = 20741 m= 726 mr = 4188 m= 21 mr = 428 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 6283 time to turn everything in is 0.5400000 number of dielectric boundary points 32827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14405 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) : 0.7232685 object centre at (A) : 1.264500 -1.039501 -1.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4282176E-02 -3.5654638E-02 midg,1,midg; midg,igrid,midg -6.1593791E-03 4.8904948E-02 1,midg,midg; igrid,midg,midg -6.4496353E-02 6.3151168E-03 gauss-seidel spectral radius is 0.9988735 estimated iterations to convergence 236 setup time was (sec) 0.8200000 now iterating at: 14:07:55 rms-change max change #iterations 4.628264 197.0592 at 10iterations 2.311908 80.86621 at 20iterations 1.157440 44.03446 at 30iterations 0.5816532 18.28981 at 40iterations 0.2923596 9.406296 at 50iterations 0.1459589 4.317955 at 60iterations 7.3441699E-02 2.352985 at 70iterations 3.6732208E-02 1.124126 at 80iterations 1.8408882E-02 0.5191132 at 90iterations 9.2495782E-03 0.2549343 at 100iterations 4.6362928E-03 0.1501443 at 110iterations 2.3263777E-03 7.0605755E-02 at 120iterations finished qdiffx linear iterations at : 14:08:01 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 2.3263777E-03 7.0605755E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 14:08:02 7.379u 0.228s 0:07.99 94.9% 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 Mon Oct 10 2011 at 14:08:02 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 3.254708 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): -23.34600 25.87500 ymin,ymax (A): -23.13300 21.05400 zmin,zma (A): -24.03900 20.34600 x,y,z range (A): 49.22100 44.18700 44.38500 scale (grids/A): 3.254708 object centre (A): 1.264500 -1.039501 -1.846500 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : -1.499990 assigned positive charge : 284.9172 centred at (gu) : 88.29871 91.93726 94.38129 assigned negative charge : -286.4171 centred at (gu) : 87.63208 90.91364 94.60616 start vw surface at 0.1400000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 167173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17911 grid for indexing accessible points = 1.400000 m= 85643 mr = 118257 m= 36378 mr = 70238 m= 11811 mr = 29912 m= 2916 mr = 9337 m= 395 mr = 2255 m= 21 mr = 255 m= 0 mr = 7 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 20575 time to turn everything in is 1.670000 number of dielectric boundary points 74076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 14480 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) : 2.169806 object centre at (A) : 1.264500 -1.039501 -1.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4140528 -0.3859888 midg,1,midg; midg,igrid,midg -1.4817080E-02 0.4592788 1,midg,midg; igrid,midg,midg -0.6768775 -0.1349817 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 1.970000 now iterating at: 14:08:04 rms-change max change #iterations 10.03417 331.0331 at 10iterations 5.891976 125.5058 at 20iterations 3.434098 62.48388 at 30iterations 2.005355 35.12305 at 40iterations 1.172216 21.38637 at 50iterations 0.6827300 11.59227 at 60iterations 0.3978031 6.444447 at 70iterations 0.2320427 4.019299 at 80iterations 0.1352011 2.225518 at 90iterations 7.9054967E-02 1.336855 at 100iterations 4.5873862E-02 0.7941208 at 110iterations 2.6712511E-02 0.4906545 at 120iterations 1.5588158E-02 0.2696381 at 130iterations 9.0834619E-03 0.1614685 at 140iterations 5.3133620E-03 9.6345901E-02 at 150iterations 3.0872351E-03 5.2181244E-02 at 160iterations 1.8007928E-03 3.1276941E-02 at 170iterations 1.0523719E-03 1.8436432E-02 at 180iterations finished qdiffx linear iterations at : 14:08:14 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 1.0523719E-03 1.8436432E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:08:16 12.323u 0.205s 0:13.52 92.6% 0+0k 0+0io 0pf+0w