Thu Jan 19 13:34:05 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:07 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4225920 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 0.4225920 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1033.629 centred at (gu) : 91.20253 89.91657 91.54727 assigned negative charge : -1041.429 centred at (gu) : 91.17932 89.96455 91.61115 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 136208 no. pairs analyzed = 136208 no. exposed pairs = 8927 no. arc points = 60881 no. surface atoms = 2995 nbur = 3834 mkacc time = 0.2300000 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 = 1.988000 m= 195 mr = 3495 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4974 ## 1085 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10115 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6107063E-13 -5.7666250E-12 midg,1,midg; midg,igrid,midg 9.8557317E-13 -2.8021045E-12 1,midg,midg; igrid,midg,midg -1.2913984E-12 -9.2587333E-15 gauss-seidel spectral radius is 0.9716048 estimated iterations to convergence 50 setup time was (sec) 0.6300000 now iterating at: 13:34:08 rms-change max change #iterations 2.9059840E-02 4.652878 at 10iterations 2.4085809E-03 0.3996754 at 20iterations 9.0612908E-04 0.1590757 at 30iterations 3.6920074E-04 6.5702438E-02 at 40iterations 1.5084870E-04 2.6919365E-02 at 50iterations finished qdiffx linear iterations at : 13:34:13 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 1.5084870E-04 2.6919365E-02 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:34:14 3.822u 0.191s 0:07.56 53.0% 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 Thu Jan 19 2012 at 13:34:15 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.267776 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 1.267776 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1033.629 centred at (gu) : 93.60541 89.74816 94.64017 assigned negative charge : -1041.429 centred at (gu) : 93.53780 89.89325 94.83288 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 86581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60881 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19960 mr = 57311 m= 940 mr = 11755 m= 5 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4800000 number of dielectric boundary points 38272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1120 ## 45 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 45847 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) : 0.4225920 object centre at (A) : -29.26550 56.88600 -0.8210011 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0924761E-03 -8.5234791E-03 midg,1,midg; midg,igrid,midg -1.1126642E-03 -6.8668928E-03 1,midg,midg; igrid,midg,midg -2.3876240E-04 -1.1169127E-03 gauss-seidel spectral radius is 0.9973080 estimated iterations to convergence 154 setup time was (sec) 0.7400000 now iterating at: 13:34:20 rms-change max change #iterations 2.945378 124.3052 at 10iterations 1.020160 36.97076 at 20iterations 0.3517780 14.43523 at 30iterations 0.1216526 4.324699 at 40iterations 4.2199712E-02 1.501099 at 50iterations 1.4785936E-02 0.5300369 at 60iterations 5.3765164E-03 0.2300063 at 70iterations 2.2108778E-03 8.0276489E-02 at 80iterations 1.1574432E-03 4.6646118E-02 at 90iterations 7.4486341E-04 2.7559280E-02 at 100iterations 5.2462361E-04 1.9408226E-02 at 110iterations 3.7838353E-04 1.3973236E-02 at 120iterations finished qdiffx linear iterations at : 13:34:42 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 3.7838353E-04 1.3973236E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 13:34:43 8.677u 0.237s 0:27.39 32.4% 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 Thu Jan 19 2012 at 13:34:43 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: 356 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6829 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.901664 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): -61.98600 3.455000 ymin,ymax (A): 17.69600 96.07600 zmin,zma (A): -42.94200 41.30000 x,y,z range (A): 65.44100 78.38000 84.24200 scale (grids/A): 1.901664 object centre (A): -29.26550 56.88600 -0.8210011 number of atom coordinates read : 6829 total number of charged atoms : 6659 net assigned charge : -7.791947 assigned positive charge : 1033.629 centred at (gu) : 95.40751 89.62149 96.95974 assigned negative charge : -1041.429 centred at (gu) : 95.30666 89.83964 97.24933 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 203682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60881 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 77988 mr = 143697 m= 13643 mr = 57273 m= 868 mr = 8458 m= 16 mr = 265 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 192 time to turn everything in is 1.030000 number of dielectric boundary points 86505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 52458 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) : 1.267776 object centre at (A) : -29.26550 56.88600 -0.8210011 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8033527E-02 -0.1251856 midg,1,midg; midg,igrid,midg -1.7180281E-02 -0.2380116 1,midg,midg; igrid,midg,midg -6.2557268E-03 -4.5810402E-03 gauss-seidel spectral radius is 0.9989500 estimated iterations to convergence 244 setup time was (sec) 1.290000 now iterating at: 13:34:44 rms-change max change #iterations 9.245286 258.5366 at 10iterations 4.974951 134.8170 at 20iterations 2.654531 74.13112 at 30iterations 1.404497 35.87710 at 40iterations 0.7382072 19.49643 at 50iterations 0.3875073 9.234787 at 60iterations 0.2028966 5.099986 at 70iterations 0.1058284 2.476280 at 80iterations 5.5157688E-02 1.192982 at 90iterations 2.8672684E-02 0.5841436 at 100iterations 1.4907610E-02 0.3458748 at 110iterations 7.7783903E-03 0.1719952 at 120iterations 4.0591815E-03 9.5701218E-02 at 130iterations 2.1425965E-03 4.3577194E-02 at 140iterations 1.1519062E-03 2.4815559E-02 at 150iterations 6.4596452E-04 1.4780998E-02 at 160iterations 3.8785645E-04 9.1123581E-03 at 170iterations 2.5349256E-04 5.8135986E-03 at 180iterations finished qdiffx linear iterations at : 13:35:14 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 2.5349256E-04 5.8135986E-03 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 13:35:16 13.492u 0.227s 0:33.02 41.5% 0+0k 0+0io 0pf+0w