Tue Nov 22 14:14:15 PST 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 Nov 22 2011 at 14:14:19 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6431100 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 0.6431100 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.16365 92.79615 90.11707 assigned negative charge : -282.5023 centred at (gu) : 90.25419 92.88175 90.04566 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5751 nv = 96 ne = 84 npr = 39233 no. pairs analyzed = 39233 no. exposed pairs = 2482 no. arc points = 17729 no. surface atoms = 846 nbur = 1120 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3221 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1600000 number of dielectric boundary points 2813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1734 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5369358E-09 1.5001305E-08 midg,1,midg; midg,igrid,midg 8.8989589E-09 -4.3161256E-11 1,midg,midg; igrid,midg,midg 1.5799154E-08 -2.3975691E-10 gauss-seidel spectral radius is 0.9874219 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 14:14:22 rms-change max change #iterations 0.1217800 18.19428 at 10iterations 1.2302728E-02 1.678607 at 20iterations 1.1995411E-03 0.1772385 at 30iterations 1.2223858E-04 1.9790649E-02 at 40iterations 1.2195922E-05 1.7528534E-03 at 50iterations finished qdiffx linear iterations at : 14:14:31 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.2195922E-05 1.7528534E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 14:14:32 3.645u 0.189s 0:14.29 26.7% 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 Tue Nov 22 2011 at 14:14:35 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.929330 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 1.929330 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.49100 98.38829 90.35122 assigned negative charge : -282.5023 centred at (gu) : 90.76282 98.64534 90.13712 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17729 grid for indexing accessible points = 1.400000 m= 24398 mr = 41486 m= 4289 mr = 19175 m= 254 mr = 2917 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 291 time to turn everything in is 0.3300000 number of dielectric boundary points 25886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14455 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) : 0.6431100 object centre at (A) : 15.61550 22.47200 3.526000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1721272E-02 1.2126315E-02 midg,1,midg; midg,igrid,midg 3.0490253E-02 1.2743206E-03 1,midg,midg; igrid,midg,midg 8.6108940E-03 9.0192193E-03 gauss-seidel spectral radius is 0.9985979 estimated iterations to convergence 212 setup time was (sec) 0.5800000 now iterating at: 14:14:40 rms-change max change #iterations 3.613646 153.7669 at 10iterations 1.673512 62.01789 at 20iterations 0.7792686 28.36730 at 30iterations 0.3611686 11.96087 at 40iterations 0.1668096 5.603798 at 50iterations 7.7361912E-02 2.645001 at 60iterations 3.5709340E-02 1.412381 at 70iterations 1.6526151E-02 0.5551634 at 80iterations 7.6963170E-03 0.2808418 at 90iterations 3.5598530E-03 0.1180682 at 100iterations 1.6520807E-03 5.4405212E-02 at 110iterations 7.6579879E-04 3.0592918E-02 at 120iterations finished qdiffx linear iterations at : 14:15:03 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 7.6579879E-04 3.0592918E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 14:15:05 8.374u 0.244s 0:29.83 28.8% 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 Nov 22 2011 at 14:15:10 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.893995 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): -5.373000 36.60400 ymin,ymax (A): -3.638000 48.58200 zmin,zma (A): -24.15200 31.20400 x,y,z range (A): 41.97700 52.22000 55.35600 scale (grids/A): 2.893995 object centre (A): 15.61550 22.47200 3.526000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 287.5021 centred at (gu) : 90.73653 102.5824 90.52668 assigned negative charge : -282.5023 centred at (gu) : 91.14427 102.9681 90.20569 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 139593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17729 grid for indexing accessible points = 1.400000 m= 75598 mr = 99897 m= 31434 mr = 63631 m= 7907 mr = 26729 m= 1085 mr = 6173 m= 73 mr = 796 m= 0 mr = 29 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 849 time to turn everything in is 0.8300000 number of dielectric boundary points 58435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14668 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) : 1.929330 object centre at (A) : 15.61550 22.47200 3.526000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7130338 -2.8789500E-02 midg,1,midg; midg,igrid,midg 0.3032373 -6.1546758E-02 1,midg,midg; igrid,midg,midg 4.8694637E-02 0.1483718 gauss-seidel spectral radius is 0.9992368 estimated iterations to convergence 286 setup time was (sec) 1.110000 now iterating at: 14:15:16 rms-change max change #iterations 8.454684 335.8231 at 10iterations 4.847291 143.8068 at 20iterations 2.760458 82.06201 at 30iterations 1.571341 36.90060 at 40iterations 0.8968012 21.33452 at 50iterations 0.5093341 10.40356 at 60iterations 0.2907073 6.373430 at 70iterations 0.1655048 3.554600 at 80iterations 9.4002292E-02 1.913997 at 90iterations 5.3472154E-02 1.052193 at 100iterations 3.0372554E-02 0.5929794 at 110iterations 1.7272362E-02 0.3836060 at 120iterations 9.8176282E-03 0.1882420 at 130iterations 5.5740415E-03 0.1149597 at 140iterations 3.1745234E-03 6.1259270E-02 at 150iterations 1.8105452E-03 3.6845945E-02 at 160iterations 1.0262498E-03 2.1609306E-02 at 170iterations 5.8305659E-04 1.3412476E-02 at 180iterations finished qdiffx linear iterations at : 14:15:53 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 5.8305659E-04 1.3412476E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 14:15:55 13.527u 0.279s 0:45.41 30.3% 0+0k 0+0io 0pf+0w