Sat Oct 8 11:35:31 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+sph.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 = amb.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 8 2011 at 11:35:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 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: 0.5707598 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 0.5707598 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 687.6226 centred at (gu) : 90.88040 89.07681 88.77930 assigned negative charge : -693.1262 centred at (gu) : 90.71587 89.18436 88.94978 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9451 nv = 96 ne = 84 npr = 96591 no. pairs analyzed = 96591 no. exposed pairs = 5043 no. arc points = 34744 no. surface atoms = 1711 nbur = 2850 mkacc time = 0.2700000 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 = 1.484000 m= 413 mr = 5511 m= 0 mr = 37 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.5400000 number of dielectric boundary points 4316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3571 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12455 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3353028E-09 -3.9988932E-09 midg,1,midg; midg,igrid,midg 2.1164117E-09 -2.9839626E-09 1,midg,midg; igrid,midg,midg -4.2094643E-09 3.8071177E-09 gauss-seidel spectral radius is 0.9842705 estimated iterations to convergence 66 setup time was (sec) 0.8300000 now iterating at: 11:35:33 rms-change max change #iterations 0.1155503 16.80179 at 10iterations 8.8617681E-03 1.279417 at 20iterations 8.7896781E-04 0.1083927 at 30iterations 1.6793085E-04 2.2704124E-02 at 40iterations 5.3002314E-05 7.4994564E-03 at 50iterations finished qdiffx linear iterations at : 11:35:36 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 5.3002314E-05 7.4994564E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 11:35:36 4.399u 0.272s 0:05.01 93.0% 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 Sat Oct 8 2011 at 11:35:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 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: 1.712279 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 1.712279 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 687.6226 centred at (gu) : 92.63972 87.22886 86.33689 assigned negative charge : -693.1262 centred at (gu) : 92.14688 87.55231 86.84892 start vw surface at 0.2000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 105247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34744 grid for indexing accessible points = 1.400000 m= 35291 mr = 76497 m= 4521 mr = 26156 m= 151 mr = 2684 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 7731 time to turn everything in is 0.8900000 number of dielectric boundary points 39839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 34074 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) : 0.5707598 object centre at (A) : 3.855499 64.95800 60.49500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1280583E-02 -3.0964531E-02 midg,1,midg; midg,igrid,midg 1.9545887E-02 -1.8091723E-02 1,midg,midg; igrid,midg,midg -2.7505618E-02 3.5788782E-02 gauss-seidel spectral radius is 0.9984872 estimated iterations to convergence 204 setup time was (sec) 1.210000 now iterating at: 11:35:38 rms-change max change #iterations 4.752663 179.4739 at 10iterations 2.133839 66.18314 at 20iterations 0.9634551 27.00363 at 30iterations 0.4337876 14.43816 at 40iterations 0.1949706 5.055749 at 50iterations 8.8437267E-02 2.406570 at 60iterations 3.9826691E-02 1.083309 at 70iterations 1.8016055E-02 0.5246887 at 80iterations 8.1268074E-03 0.2264605 at 90iterations 3.6888993E-03 0.1064339 at 100iterations 1.6820719E-03 4.7420502E-02 at 110iterations 7.7458407E-04 2.1778107E-02 at 120iterations finished qdiffx linear iterations at : 11:35:47 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 7.7458407E-04 2.1778107E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.23000 DelPhi exited at 11:35:47 10.236u 0.321s 0:10.84 97.3% 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 8 2011 at 11:35:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4561 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: 2.568419 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): -27.33100 35.04200 ymin,ymax (A): 34.89600 95.02000 zmin,zma (A): 30.43100 90.55900 x,y,z range (A): 62.37300 60.12400 60.12800 scale (grids/A): 2.568419 object centre (A): 3.855499 64.95800 60.49500 number of atom coordinates read : 4561 total number of charged atoms : 4400 net assigned charge : -5.499943 assigned positive charge : 687.6226 centred at (gu) : 93.95930 85.84267 84.50491 assigned negative charge : -693.1262 centred at (gu) : 93.22013 86.32838 85.27331 start vw surface at 0.2200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 244550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34744 grid for indexing accessible points = 1.400000 m= 119878 mr = 185413 m= 37731 mr = 99201 m= 7719 mr = 30122 m= 835 mr = 5863 m= 14 mr = 494 m= 0 mr = 2 time to grow re-entrant surface = 1.370000 no. cavity mid-points inaccessible to solvent = 25606 time to turn everything in is 2.290000 number of dielectric boundary points 89632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 35169 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) : 1.712279 object centre at (A) : 3.855499 64.95800 60.49500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2971130 -0.3694507 midg,1,midg; midg,igrid,midg 0.2970169 -0.3079528 1,midg,midg; igrid,midg,midg -0.1963061 0.3338459 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 2.640000 now iterating at: 11:35:50 rms-change max change #iterations 11.60993 341.8641 at 10iterations 6.758639 138.1209 at 20iterations 3.918781 68.90361 at 30iterations 2.265775 42.15481 at 40iterations 1.304996 22.32801 at 50iterations 0.7533370 13.45466 at 60iterations 0.4325074 6.883411 at 70iterations 0.2483100 3.868671 at 80iterations 0.1424171 2.330981 at 90iterations 8.1545800E-02 1.265110 at 100iterations 4.6795703E-02 0.7800803 at 110iterations 2.6821077E-02 0.4554672 at 120iterations 1.5376816E-02 0.2373638 at 130iterations 8.8125393E-03 0.1345739 at 140iterations 5.0617703E-03 7.8854561E-02 at 150iterations 2.9110680E-03 4.6244621E-02 at 160iterations 1.6814128E-03 2.7179718E-02 at 170iterations 9.7704201E-04 1.6654968E-02 at 180iterations finished qdiffx linear iterations at : 11:36:05 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 9.7704201E-04 1.6654968E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 11:36:06 17.869u 0.349s 0:18.54 98.1% 0+0k 0+0io 0pf+0w