Sun Oct 9 16:40:39 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+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 Sun Oct 9 2011 at 16:40:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5853242 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 0.5853242 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3426 net assigned charge : -0.4999894 assigned positive charge : 532.4979 centred at (gu) : 89.62223 89.61175 92.06035 assigned negative charge : -532.9999 centred at (gu) : 89.62836 89.60468 91.90356 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8287 nv = 96 ne = 84 npr = 68870 no. pairs analyzed = 68870 no. exposed pairs = 5327 no. arc points = 37772 no. surface atoms = 1744 nbur = 1834 mkacc time = 0.1500000 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 = 1.456000 m= 425 mr = 3862 m= 0 mr = 28 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 4822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3770 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2399878E-09 7.5023721E-09 midg,1,midg; midg,igrid,midg -5.0545085E-10 -1.8068002E-11 1,midg,midg; igrid,midg,midg -5.2460265E-11 -3.9587134E-10 gauss-seidel spectral radius is 0.9850008 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 16:40:40 rms-change max change #iterations 0.1076994 16.07103 at 10iterations 8.6859204E-03 1.390186 at 20iterations 6.9497526E-04 9.0061188E-02 at 30iterations 6.4877800E-05 1.0628939E-02 at 40iterations 1.2229998E-05 1.5296936E-03 at 50iterations finished qdiffx linear iterations at : 16:40:42 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.2229998E-05 1.5296936E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 16:40:43 3.127u 0.152s 0:03.64 89.8% 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 Sun Oct 9 2011 at 16:40:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.755973 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 1.755973 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3426 net assigned charge : -0.4999894 assigned positive charge : 532.4979 centred at (gu) : 88.86562 88.83442 96.18032 assigned negative charge : -532.9999 centred at (gu) : 88.88427 88.81370 95.71053 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37772 grid for indexing accessible points = 1.400000 m= 28793 mr = 56720 m= 4059 mr = 18714 m= 198 mr = 2065 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 44714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 26645 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) : 0.5853242 object centre at (A) : -45.93100 18.63950 -40.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1554680E-02 -1.8245481E-02 midg,1,midg; midg,igrid,midg 4.0082401E-03 1.4321222E-03 1,midg,midg; igrid,midg,midg -9.7048428E-04 -7.2996174E-03 gauss-seidel spectral radius is 0.9985308 estimated iterations to convergence 207 setup time was (sec) 0.9200000 now iterating at: 16:40:44 rms-change max change #iterations 4.321662 199.8964 at 10iterations 1.950782 61.33940 at 20iterations 0.8809598 30.92201 at 30iterations 0.4001969 14.02434 at 40iterations 0.1820938 5.502089 at 50iterations 8.3007097E-02 2.556396 at 60iterations 3.7564006E-02 1.109436 at 70iterations 1.7111903E-02 0.5673265 at 80iterations 7.7752997E-03 0.2360096 at 90iterations 3.5446943E-03 0.1104393 at 100iterations 1.6190313E-03 4.9739838E-02 at 110iterations 7.3946477E-04 2.2325516E-02 at 120iterations finished qdiffx linear iterations at : 16:40:51 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 7.3946477E-04 2.2325516E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 16:40:51 8.076u 0.173s 0:08.56 96.2% 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 Sun Oct 9 2011 at 16:40:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.633959 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): -74.43501 -17.42700 ymin,ymax (A): -11.77100 49.05000 zmin,zma (A): -70.51400 -9.960000 x,y,z range (A): 57.00800 60.82100 60.55400 scale (grids/A): 2.633959 object centre (A): -45.93100 18.63950 -40.23700 number of atom coordinates read : 3578 total number of charged atoms : 3426 net assigned charge : -0.4999894 assigned positive charge : 532.4979 centred at (gu) : 88.29823 88.25136 99.27013 assigned negative charge : -532.9999 centred at (gu) : 88.32632 88.22044 98.56561 start vw surface at 0.2400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 206487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37772 grid for indexing accessible points = 1.400000 m= 94295 mr = 139995 m= 31328 mr = 70877 m= 6703 mr = 23013 m= 736 mr = 4398 m= 21 mr = 379 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 100905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 27401 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) : 1.755973 object centre at (A) : -45.93100 18.63950 -40.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4449376 -0.1717768 midg,1,midg; midg,igrid,midg -0.1134557 -0.1466034 1,midg,midg; igrid,midg,midg -3.3563219E-02 -0.1280401 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 1.870000 now iterating at: 16:40:54 rms-change max change #iterations 11.05458 324.4693 at 10iterations 6.679604 160.8492 at 20iterations 3.993746 90.81139 at 30iterations 2.366985 48.82185 at 40iterations 1.396135 29.91095 at 50iterations 0.8217083 16.46507 at 60iterations 0.4817220 9.272374 at 70iterations 0.2815604 5.396851 at 80iterations 0.1638582 3.062766 at 90iterations 9.5314696E-02 1.733072 at 100iterations 5.5431094E-02 1.039856 at 110iterations 3.2232836E-02 0.5716716 at 120iterations 1.8722309E-02 0.3580503 at 130iterations 1.0841128E-02 0.2288040 at 140iterations 6.2892875E-03 0.1161351 at 150iterations 3.6398133E-03 6.6282272E-02 at 160iterations 2.1111285E-03 3.5934448E-02 at 170iterations 1.2246625E-03 2.2453308E-02 at 180iterations finished qdiffx linear iterations at : 16:41:04 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 1.2246625E-03 2.2453308E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 16:41:04 12.308u 0.189s 0:12.83 97.2% 0+0k 0+0io 0pf+0w