Mon Oct 10 14:13:39 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 14:13:39 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 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: 0.6481094 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): -10.55500 37.79800 ymin,ymax (A): -0.1170000 54.81200 zmin,zma (A): -23.98800 26.75200 x,y,z range (A): 48.35300 54.92900 50.74000 scale (grids/A): 0.6481094 object centre (A): 13.62150 27.34750 1.382000 number of atom coordinates read : 2788 total number of charged atoms : 2415 net assigned charge : 5.500031 assigned positive charge : 376.4836 centred at (gu) : 89.66766 89.66048 89.70144 assigned negative charge : -370.9847 centred at (gu) : 89.74908 89.63554 89.64565 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7415 nv = 96 ne = 84 npr = 50598 no. pairs analyzed = 50598 no. exposed pairs = 3452 no. arc points = 24250 no. surface atoms = 1157 nbur = 1631 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3892 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2315 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4113223E-09 1.6701660E-08 midg,1,midg; midg,igrid,midg 7.0748731E-09 1.2615600E-08 1,midg,midg; igrid,midg,midg 2.2824514E-08 -1.1860816E-09 gauss-seidel spectral radius is 0.9876680 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 14:13:40 rms-change max change #iterations 0.1476489 20.76595 at 10iterations 1.5030448E-02 2.052750 at 20iterations 1.5197924E-03 0.2129822 at 30iterations 1.5446200E-04 2.3620605E-02 at 40iterations 1.5724687E-05 2.1667480E-03 at 50iterations finished qdiffx linear iterations at : 14:13:43 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.5724687E-05 2.1667480E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:13:43 3.345u 0.152s 0:03.84 90.8% 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 Mon Oct 10 2011 at 14:13:43 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 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: 1.944328 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): -10.55500 37.79800 ymin,ymax (A): -0.1170000 54.81200 zmin,zma (A): -23.98800 26.75200 x,y,z range (A): 48.35300 54.92900 50.74000 scale (grids/A): 1.944328 object centre (A): 13.62150 27.34750 1.382000 number of atom coordinates read : 2788 total number of charged atoms : 2415 net assigned charge : 5.500031 assigned positive charge : 376.4836 centred at (gu) : 89.00224 88.98059 89.10376 assigned negative charge : -370.9847 centred at (gu) : 89.24696 88.90659 88.93660 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24250 grid for indexing accessible points = 1.400000 m= 28603 mr = 54495 m= 4807 mr = 20307 m= 375 mr = 2779 m= 10 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18885 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) : 0.6481094 object centre at (A) : 13.62150 27.34750 1.382000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2186958E-04 1.3306439E-02 midg,1,midg; midg,igrid,midg -1.5514023E-03 9.3851369E-03 1,midg,midg; igrid,midg,midg 3.5859853E-02 1.0531353E-02 gauss-seidel spectral radius is 0.9986961 estimated iterations to convergence 219 setup time was (sec) 0.6200000 now iterating at: 14:13:44 rms-change max change #iterations 4.333667 186.2569 at 10iterations 2.064849 70.38045 at 20iterations 0.9823529 31.58638 at 30iterations 0.4691410 15.35091 at 40iterations 0.2238775 7.561141 at 50iterations 0.1063797 3.590752 at 60iterations 5.0701186E-02 1.544021 at 70iterations 2.4214922E-02 0.7724838 at 80iterations 1.1525877E-02 0.3513470 at 90iterations 5.4971240E-03 0.1712685 at 100iterations 2.6172451E-03 8.1497192E-02 at 110iterations 1.2517826E-03 4.1702271E-02 at 120iterations finished qdiffx linear iterations at : 14:13:51 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.2517826E-03 4.1702271E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 14:13:51 7.745u 0.171s 0:08.41 94.0% 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 Mon Oct 10 2011 at 14:13:52 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2788 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: 2.916492 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): -10.55500 37.79800 ymin,ymax (A): -0.1170000 54.81200 zmin,zma (A): -23.98800 26.75200 x,y,z range (A): 48.35300 54.92900 50.74000 scale (grids/A): 2.916492 object centre (A): 13.62150 27.34750 1.382000 number of atom coordinates read : 2788 total number of charged atoms : 2415 net assigned charge : 5.500031 assigned positive charge : 376.4836 centred at (gu) : 88.50323 88.47073 88.65559 assigned negative charge : -370.9847 centred at (gu) : 88.87042 88.35989 88.40498 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24250 grid for indexing accessible points = 1.400000 m= 92530 mr = 132580 m= 33617 mr = 74405 m= 8548 mr = 25820 m= 1654 mr = 6164 m= 156 mr = 1072 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 81033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 19310 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) : 1.944328 object centre at (A) : 13.62150 27.34750 1.382000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4633185E-02 0.1237262 midg,1,midg; midg,igrid,midg -6.9937713E-02 5.1034328E-02 1,midg,midg; igrid,midg,midg 0.3362158 0.1689977 gauss-seidel spectral radius is 0.9992842 estimated iterations to convergence 295 setup time was (sec) 1.240000 now iterating at: 14:13:53 rms-change max change #iterations 10.20919 472.7367 at 10iterations 6.038793 136.0074 at 20iterations 3.552025 69.09946 at 30iterations 2.088145 41.04533 at 40iterations 1.222520 23.11517 at 50iterations 0.7156219 13.67789 at 60iterations 0.4174133 7.840041 at 70iterations 0.2438418 5.068505 at 80iterations 0.1416524 2.830932 at 90iterations 8.2431056E-02 1.620842 at 100iterations 4.7938392E-02 0.8783817 at 110iterations 2.7851669E-02 0.5609283 at 120iterations 1.6214207E-02 0.3000741 at 130iterations 9.4269011E-03 0.1770236 at 140iterations 5.4618116E-03 0.1002541 at 150iterations 3.1692556E-03 5.6297302E-02 at 160iterations 1.8415441E-03 3.2081604E-02 at 170iterations 1.0695134E-03 2.0597160E-02 at 180iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 1.0695134E-03 2.0597160E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 14:14:05 12.637u 0.210s 0:13.15 97.6% 0+0k 0+0io 0pf+0w