Sat Oct 15 14:26:40 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 Sat Oct 15 2011 at 14:26:40 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 = 2953 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: 0.5465823 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 0.5465823 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.499960 assigned positive charge : 440.4010 centred at (gu) : 89.61481 89.68727 89.51678 assigned negative charge : -444.9021 centred at (gu) : 89.53646 89.84335 89.46809 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5660 nv = 96 ne = 84 npr = 59369 no. pairs analyzed = 59369 no. exposed pairs = 3840 no. arc points = 27160 no. surface atoms = 1307 nbur = 1646 mkacc time = 0.1000000 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 = 1.596000 m= 235 mr = 2825 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3066 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2764 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9719158E-10 3.7513197E-11 midg,1,midg; midg,igrid,midg 8.1909796E-10 -1.2659949E-09 1,midg,midg; igrid,midg,midg -9.0643221E-10 2.1903407E-10 gauss-seidel spectral radius is 0.9827434 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 14:26:41 rms-change max change #iterations 7.1522482E-02 14.44816 at 10iterations 4.8097800E-03 0.8697176 at 20iterations 3.1820845E-04 5.5017471E-02 at 30iterations 2.1693622E-05 3.3187866E-03 at 40iterations 1.4721687E-06 2.5558472E-04 at 50iterations finished qdiffx linear iterations at : 14:26:44 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.4721687E-06 2.5558472E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 14:26:44 3.499u 0.199s 0:04.20 87.6% 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 Sat Oct 15 2011 at 14:26:44 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 = 2953 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: 1.639747 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 1.639747 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.499960 assigned positive charge : 440.4010 centred at (gu) : 88.84361 89.06084 88.54988 assigned negative charge : -444.9021 centred at (gu) : 88.60921 89.52998 88.40401 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27160 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18709 mr = 41332 m= 1721 mr = 12687 m= 30 mr = 716 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 508 time to turn everything in is 0.3200000 number of dielectric boundary points 28480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21555 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) : 0.5465823 object centre at (A) : 30.53700 35.38000 16.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9633773E-03 -1.5336073E-03 midg,1,midg; midg,igrid,midg 8.9047356E-03 -1.6522521E-02 1,midg,midg; igrid,midg,midg -2.2944504E-02 9.2693893E-03 gauss-seidel spectral radius is 0.9981992 estimated iterations to convergence 187 setup time was (sec) 0.5500000 now iterating at: 14:26:45 rms-change max change #iterations 3.349293 169.0958 at 10iterations 1.392126 52.17999 at 20iterations 0.5807365 20.75928 at 30iterations 0.2437638 9.261402 at 40iterations 0.1019238 3.769022 at 50iterations 4.2507898E-02 1.629234 at 60iterations 1.7667450E-02 0.7029858 at 70iterations 7.4024000E-03 0.2768459 at 80iterations 3.1017889E-03 0.1151104 at 90iterations 1.2972406E-03 4.7126770E-02 at 100iterations 5.4299325E-04 1.8608093E-02 at 110iterations 2.2708863E-04 8.8393688E-03 at 120iterations finished qdiffx linear iterations at : 14:26:59 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.2708863E-04 8.8393688E-03 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 14:27:00 7.952u 0.222s 0:15.74 51.9% 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 Sat Oct 15 2011 at 14:27:00 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 = 2953 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: 2.459620 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): -2.029000 63.10300 ymin,ymax (A): 11.88600 58.87400 zmin,zma (A): -7.750000 39.86800 x,y,z range (A): 65.13200 46.98800 47.61800 scale (grids/A): 2.459620 object centre (A): 30.53700 35.38000 16.05900 number of atom coordinates read : 2953 total number of charged atoms : 2812 net assigned charge : -4.499960 assigned positive charge : 440.4010 centred at (gu) : 88.26530 88.59117 87.82440 assigned negative charge : -444.9021 centred at (gu) : 87.91365 89.29484 87.60580 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 145586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27160 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65235 mr = 101553 m= 18132 mr = 50818 m= 2624 mr = 13394 m= 136 mr = 1605 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1753 time to turn everything in is 0.7700000 number of dielectric boundary points 64302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22478 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) : 1.639747 object centre at (A) : 30.53700 35.38000 16.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5053951E-02 -2.7058328E-02 midg,1,midg; midg,igrid,midg 0.1514435 -0.2244014 1,midg,midg; igrid,midg,midg -0.5472205 0.5074433 gauss-seidel spectral radius is 0.9991467 estimated iterations to convergence 270 setup time was (sec) 1.010000 now iterating at: 14:27:02 rms-change max change #iterations 8.671817 325.2653 at 10iterations 4.867736 124.7486 at 20iterations 2.722135 81.25392 at 30iterations 1.515732 39.46021 at 40iterations 0.8403529 18.50404 at 50iterations 0.4662217 10.97945 at 60iterations 0.2575796 5.370110 at 70iterations 0.1421191 3.015673 at 80iterations 7.8459032E-02 1.751488 at 90iterations 4.3342710E-02 0.9494586 at 100iterations 2.3881273E-02 0.5111754 at 110iterations 1.3182560E-02 0.2723284 at 120iterations 7.2560566E-03 0.1549129 at 130iterations 3.9988481E-03 0.1002808 at 140iterations 2.2041907E-03 4.2804718E-02 at 150iterations 1.2111177E-03 2.4291992E-02 at 160iterations 6.6908309E-04 1.3882838E-02 at 170iterations 3.6892763E-04 7.3862076E-03 at 180iterations finished qdiffx linear iterations at : 14:27:25 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 3.6892763E-04 7.3862076E-03 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 14:27:26 12.846u 0.257s 0:25.73 50.8% 0+0k 0+0io 0pf+0w