Wed Feb 15 08:54:48 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:48 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 = 2651 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5733335 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 0.5733335 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 87.61639 90.16259 89.71496 assigned negative charge : -394.4395 centred at (gu) : 87.90131 90.29728 89.88428 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5635 nv = 96 ne = 84 npr = 54593 no. pairs analyzed = 54593 no. exposed pairs = 3175 no. arc points = 22482 no. surface atoms = 1074 nbur = 1577 mkacc time = 0.1300000 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 = 1.512000 m= 230 mr = 3054 m= 0 mr = 15 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3200000 number of dielectric boundary points 2796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2256 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7248 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5584398E-09 -1.8083368E-09 midg,1,midg; midg,igrid,midg 2.7000340E-09 -1.4383912E-09 1,midg,midg; igrid,midg,midg 8.9513508E-09 -2.1626949E-09 gauss-seidel spectral radius is 0.9842692 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 08:54:49 rms-change max change #iterations 8.6840972E-02 14.24546 at 10iterations 7.5110747E-03 1.349968 at 20iterations 9.7262010E-04 0.2360916 at 30iterations 2.0749554E-04 5.3966522E-02 at 40iterations 4.8096197E-05 1.2729645E-02 at 50iterations finished qdiffx linear iterations at : 08:54:52 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.8096197E-05 1.2729645E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:54:56 3.384u 0.155s 0:08.17 43.2% 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 Wed Feb 15 2012 at 08:54:56 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 = 2651 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.720001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 1.720001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 82.84860 90.48688 89.14423 assigned negative charge : -394.4395 centred at (gu) : 83.70383 90.89162 89.65235 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22482 grid for indexing accessible points = 1.400000 m= 19799 mr = 43471 m= 2290 mr = 14186 m= 42 mr = 1213 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1541 time to turn everything in is 0.4800000 number of dielectric boundary points 25832 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19424 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) : 0.5733335 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4667385E-02 -2.2629747E-05 midg,1,midg; midg,igrid,midg 1.9390840E-02 -1.8573113E-02 1,midg,midg; igrid,midg,midg 4.1800928E-03 -1.2807825E-02 gauss-seidel spectral radius is 0.9983273 estimated iterations to convergence 194 setup time was (sec) 0.7700000 now iterating at: 08:54:57 rms-change max change #iterations 3.434618 141.1799 at 10iterations 1.476738 56.01433 at 20iterations 0.6385221 22.78792 at 30iterations 0.2766716 11.79104 at 40iterations 0.1192398 4.415433 at 50iterations 5.1668629E-02 2.099731 at 60iterations 2.2531012E-02 0.8189697 at 70iterations 9.8509239E-03 0.3356133 at 80iterations 4.3579210E-03 0.1794720 at 90iterations 1.9825499E-03 7.8453064E-02 at 100iterations 9.3296211E-04 4.1683197E-02 at 110iterations 4.6243699E-04 2.0549774E-02 at 120iterations finished qdiffx linear iterations at : 08:55:04 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 4.6243699E-04 2.0549774E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 08:55:04 7.495u 0.182s 0:08.05 95.2% 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 Wed Feb 15 2012 at 08:55:05 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 = 2651 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.580001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 2.580001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 79.27284 90.73025 88.71610 assigned negative charge : -394.4395 centred at (gu) : 80.55572 91.33743 89.47867 start vw surface at 0.1800000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 145412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22482 grid for indexing accessible points = 1.400000 m= 67844 mr = 105797 m= 20243 mr = 54806 m= 3590 mr = 15912 m= 266 mr = 2556 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 5381 time to turn everything in is 1.150000 number of dielectric boundary points 58147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20058 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) : 1.720001 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1627217 8.5867718E-03 midg,1,midg; midg,igrid,midg 0.1910829 -0.4215213 1,midg,midg; igrid,midg,midg -6.3855357E-02 -0.1866765 gauss-seidel spectral radius is 0.9991677 estimated iterations to convergence 274 setup time was (sec) 1.450000 now iterating at: 08:55:06 rms-change max change #iterations 8.573406 330.6545 at 10iterations 4.798836 134.1693 at 20iterations 2.681275 55.44919 at 30iterations 1.496282 31.71479 at 40iterations 0.8314661 18.49784 at 50iterations 0.4631288 9.066269 at 60iterations 0.2576854 5.188219 at 70iterations 0.1431030 3.091681 at 80iterations 7.9536013E-02 1.808815 at 90iterations 4.4342183E-02 0.9830742 at 100iterations 2.4615560E-02 0.5005226 at 110iterations 1.3740588E-02 0.2925835 at 120iterations 7.7134538E-03 0.1709633 at 130iterations 4.3532867E-03 0.1045685 at 140iterations 2.4879859E-03 6.0966492E-02 at 150iterations 1.4625203E-03 3.5041809E-02 at 160iterations 8.8522822E-04 2.2838593E-02 at 170iterations 5.6012144E-04 1.8280029E-02 at 180iterations finished qdiffx linear iterations at : 08:55:16 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 5.6012144E-04 1.8280029E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 08:55:17 11.894u 0.162s 0:12.37 97.4% 0+0k 0+0io 0pf+0w