Sun Oct 9 02:52:02 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 02:52:02 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1106 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4341199 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): -4.993000 77.01200 ymin,ymax (A): 1.273000 67.57800 zmin,zma (A): 174.6080 235.3260 x,y,z range (A): 82.00500 66.30499 60.71799 scale (grids/A): 0.4341199 object centre (A): 36.00950 34.42550 204.9670 number of atom coordinates read : 4525 total number of charged atoms : 4292 net assigned charge : 19.99999 assigned positive charge : 661.6860 centred at (gu) : 86.64156 91.14714 88.89729 assigned negative charge : -641.6907 centred at (gu) : 86.58180 91.12685 88.91646 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 5042 nv = 96 ne = 84 npr = 92083 no. pairs analyzed = 92083 no. exposed pairs = 5754 no. arc points = 39643 no. surface atoms = 1949 nbur = 2576 mkacc time = 0.2600000 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 = 1.932000 m= 148 mr = 2388 m= 0 mr = 2 time to grow re-entrant surface = 0.2799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 2800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3315 ## 737 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 6949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5204942E-12 3.0595767E-12 midg,1,midg; midg,igrid,midg 2.9811997E-12 8.7147867E-12 1,midg,midg; igrid,midg,midg 5.8816680E-12 2.9685182E-12 gauss-seidel spectral radius is 0.9729332 estimated iterations to convergence 51 setup time was (sec) 0.8800000 now iterating at: 02:52:03 rms-change max change #iterations 2.8669933E-02 4.932810 at 10iterations 2.8716985E-03 0.5977097 at 20iterations 7.3278567E-04 0.1607761 at 30iterations 1.9995266E-04 4.6724319E-02 at 40iterations 5.5018507E-05 1.3334274E-02 at 50iterations finished qdiffx linear iterations at : 02:52:06 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 5.5018507E-05 1.3334274E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 02:52:06 4.279u 0.180s 0:04.79 92.9% 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 Sun Oct 9 2011 at 02:52:06 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1106 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.302360 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): -4.993000 77.01200 ymin,ymax (A): 1.273000 67.57800 zmin,zma (A): 174.6080 235.3260 x,y,z range (A): 82.00500 66.30499 60.71799 scale (grids/A): 1.302360 object centre (A): 36.00950 34.42550 204.9670 number of atom coordinates read : 4525 total number of charged atoms : 4292 net assigned charge : 19.99999 assigned positive charge : 661.6860 centred at (gu) : 79.92283 93.43990 86.69012 assigned negative charge : -641.6907 centred at (gu) : 79.74506 93.38043 86.74870 start vw surface at 0.2400000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 59460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 13701 mr = 39078 m= 707 mr = 8192 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 451 time to turn everything in is 0.6100000 number of dielectric boundary points 26486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 737 ## 23 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 30022 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) : 0.4341199 object centre at (A) : 36.00950 34.42550 204.9670 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2958812E-03 7.8653591E-04 midg,1,midg; midg,igrid,midg 3.4617258E-03 2.6196833E-03 1,midg,midg; igrid,midg,midg 1.7835431E-02 3.2283510E-03 gauss-seidel spectral radius is 0.9972332 estimated iterations to convergence 152 setup time was (sec) 0.9600000 now iterating at: 02:52:08 rms-change max change #iterations 2.374156 118.9939 at 10iterations 0.8072469 35.06512 at 20iterations 0.2744550 11.62691 at 30iterations 9.3863532E-02 3.738928 at 40iterations 3.2577943E-02 1.349321 at 50iterations 1.1634277E-02 0.5384779 at 60iterations 4.6048146E-03 0.2110062 at 70iterations 2.1486836E-03 9.7991943E-02 at 80iterations 1.1976296E-03 5.6602478E-02 at 90iterations 7.4175157E-04 3.6561966E-02 at 100iterations 4.7652790E-04 2.3834229E-02 at 110iterations 3.1009046E-04 1.5769958E-02 at 120iterations finished qdiffx linear iterations at : 02:52:15 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 3.1009046E-04 1.5769958E-02 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 02:52:16 8.937u 0.228s 0:09.54 95.9% 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 Sun Oct 9 2011 at 02:52:16 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1106 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.953539 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): -4.993000 77.01200 ymin,ymax (A): 1.273000 67.57800 zmin,zma (A): 174.6080 235.3260 x,y,z range (A): 82.00500 66.30499 60.71799 scale (grids/A): 1.953539 object centre (A): 36.00950 34.42550 204.9670 number of atom coordinates read : 4525 total number of charged atoms : 4292 net assigned charge : 19.99999 assigned positive charge : 661.6860 centred at (gu) : 74.88409 95.15939 85.03484 assigned negative charge : -641.6907 centred at (gu) : 74.61739 95.07040 85.12295 start vw surface at 0.2400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 139625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 53239 mr = 97877 m= 9632 mr = 39086 m= 722 mr = 6107 m= 13 mr = 272 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 1572 time to turn everything in is 1.330000 number of dielectric boundary points 59889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 33873 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) : 1.302360 object centre at (A) : 36.00950 34.42550 204.9670 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0476897E-02 9.9722585E-03 midg,1,midg; midg,igrid,midg 9.7459801E-02 5.8705300E-02 1,midg,midg; igrid,midg,midg 0.4819221 4.1218299E-02 gauss-seidel spectral radius is 0.9988493 estimated iterations to convergence 233 setup time was (sec) 1.700000 now iterating at: 02:52:18 rms-change max change #iterations 7.173462 224.7345 at 10iterations 3.704702 100.8523 at 20iterations 1.899507 58.32212 at 30iterations 0.9678451 24.11833 at 40iterations 0.4914208 14.16732 at 50iterations 0.2489758 6.063929 at 60iterations 0.1258456 3.306305 at 70iterations 6.3479900E-02 1.645039 at 80iterations 3.1983100E-02 0.7687302 at 90iterations 1.6170604E-02 0.3800850 at 100iterations 8.1603853E-03 0.2026329 at 110iterations 4.1657584E-03 0.1098251 at 120iterations 2.1572795E-03 5.7926178E-02 at 130iterations 1.1505478E-03 2.7388573E-02 at 140iterations 6.4474100E-04 1.7526627E-02 at 150iterations 3.8773534E-04 1.1032104E-02 at 160iterations 2.5100107E-04 7.4825287E-03 at 170iterations 1.7226322E-04 5.1717758E-03 at 180iterations finished qdiffx linear iterations at : 02:52:30 total time elapsed so far: 13.91000 # loops : 180 mean,max change (kT/e) : 1.7226322E-04 5.1717758E-03 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.14000 DelPhi exited at 02:52:31 14.142u 0.232s 0:14.74 97.4% 0+0k 0+0io 0pf+0w