Tue Oct 11 08:41:08 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 Tue Oct 11 2011 at 08:41:08 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 = 1076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8101588 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 0.8101588 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 945 net assigned charge : 0.2280048 assigned positive charge : 148.8741 centred at (gu) : 90.27760 88.84995 89.37241 assigned negative charge : -148.6460 centred at (gu) : 90.42122 88.65389 89.32595 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4833 nv = 96 ne = 84 npr = 22112 no. pairs analyzed = 22112 no. exposed pairs = 1415 no. arc points = 10601 no. surface atoms = 474 nbur = 602 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 2447 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.1100000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 660 ## 52 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5797224E-08 9.2371188E-08 midg,1,midg; midg,igrid,midg -3.9938894E-07 2.9259522E-07 1,midg,midg; igrid,midg,midg 2.5654273E-07 -2.4248493E-07 gauss-seidel spectral radius is 0.9919423 estimated iterations to convergence 90 setup time was (sec) 0.3000000 now iterating at: 08:41:08 rms-change max change #iterations 0.2354109 38.08749 at 10iterations 3.7153345E-02 6.096315 at 20iterations 5.7904813E-03 0.9208527 at 30iterations 9.0083684E-04 0.1324940 at 40iterations 1.4246417E-04 2.0805359E-02 at 50iterations finished qdiffx linear iterations at : 08:41:11 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.4246417E-04 2.0805359E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 08:41:12 3.300u 0.174s 0:03.75 92.5% 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 Tue Oct 11 2011 at 08:41:12 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 = 1076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.430476 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 2.430476 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 945 net assigned charge : 0.2280048 assigned positive charge : 148.8741 centred at (gu) : 90.83303 86.55008 88.11762 assigned negative charge : -148.6460 centred at (gu) : 91.26381 85.96159 87.97788 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10601 grid for indexing accessible points = 1.400000 m= 19119 mr = 31909 m= 4595 mr = 14085 m= 657 mr = 3166 m= 52 mr = 418 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2212 time to turn everything in is 0.2700000 number of dielectric boundary points 24442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7545 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) : 0.8101588 object centre at (A) : 101.4255 89.27299 58.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2030750E-02 8.7359957E-03 midg,1,midg; midg,igrid,midg 3.2077951E-03 2.9569440E-02 1,midg,midg; igrid,midg,midg 1.8769508E-02 -2.1075789E-02 gauss-seidel spectral radius is 0.9989835 estimated iterations to convergence 248 setup time was (sec) 0.4800000 now iterating at: 08:41:12 rms-change max change #iterations 3.910842 238.7750 at 10iterations 2.015416 85.84582 at 20iterations 1.049106 37.69614 at 30iterations 0.5401574 18.76550 at 40iterations 0.2807279 9.417717 at 50iterations 0.1452633 4.659996 at 60iterations 7.5545125E-02 2.785160 at 70iterations 3.9088652E-02 1.312983 at 80iterations 2.0226201E-02 0.6854072 at 90iterations 1.0494269E-02 0.3749609 at 100iterations 5.4449732E-03 0.2058907 at 110iterations 2.8284634E-03 9.9756241E-02 at 120iterations finished qdiffx linear iterations at : 08:41:19 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 2.8284634E-03 9.9756241E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 08:41:20 7.669u 0.202s 0:08.50 92.4% 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 Tue Oct 11 2011 at 08:41:20 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 = 1076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.645715 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 3.645715 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 945 net assigned charge : 0.2280048 assigned positive charge : 148.8741 centred at (gu) : 91.24957 84.82507 87.17641 assigned negative charge : -148.6460 centred at (gu) : 91.89575 83.94238 86.96686 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 114036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10601 grid for indexing accessible points = 1.400000 m= 57389 mr = 77453 m= 25758 mr = 46269 m= 8960 mr = 20987 m= 2498 mr = 7095 m= 516 mr = 1942 m= 79 mr = 403 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 7367 time to turn everything in is 0.8200000 number of dielectric boundary points 55038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 7560 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) : 2.430476 object centre at (A) : 101.4255 89.27299 58.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4382127E-02 0.1486606 midg,1,midg; midg,igrid,midg 0.1230686 0.2238846 1,midg,midg; igrid,midg,midg 0.1323935 -8.1962951E-02 gauss-seidel spectral radius is 0.9993241 estimated iterations to convergence 303 setup time was (sec) 1.040000 now iterating at: 08:41:21 rms-change max change #iterations 8.204475 242.2447 at 10iterations 4.833517 131.3383 at 20iterations 2.847858 65.93860 at 30iterations 1.673138 36.41471 at 40iterations 0.9833220 19.67649 at 50iterations 0.5768675 12.01010 at 60iterations 0.3390302 6.476966 at 70iterations 0.1992299 3.866159 at 80iterations 0.1170670 2.435875 at 90iterations 6.8683207E-02 1.413483 at 100iterations 4.0357698E-02 0.7250710 at 110iterations 2.3767995E-02 0.4679565 at 120iterations 1.3885946E-02 0.2918434 at 130iterations 8.1815440E-03 0.1574745 at 140iterations 4.8094206E-03 9.8005891E-02 at 150iterations 2.8235761E-03 5.2856445E-02 at 160iterations 1.6594660E-03 3.0848503E-02 at 170iterations 9.7371032E-04 1.8962860E-02 at 180iterations finished qdiffx linear iterations at : 08:41:32 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 9.7371032E-04 1.8962860E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 08:41:33 12.153u 0.211s 0:12.70 97.3% 0+0k 0+0io 0pf+0w