Sun Oct 9 00:27:23 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 00:27:23 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 = 3383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5721541 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 0.5721541 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.50004 assigned positive charge : 499.9665 centred at (gu) : 92.03596 89.15727 88.78189 assigned negative charge : -488.4682 centred at (gu) : 92.07471 88.97594 88.70382 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7592 nv = 96 ne = 84 npr = 65049 no. pairs analyzed = 65049 no. exposed pairs = 4698 no. arc points = 33413 no. surface atoms = 1562 nbur = 1821 mkacc time = 0.1100000 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 = 1.484000 m= 343 mr = 3750 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3294 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9525 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5012568E-10 2.5511511E-09 midg,1,midg; midg,igrid,midg -1.8059541E-09 4.2899382E-09 1,midg,midg; igrid,midg,midg 1.6734908E-09 1.9734228E-09 gauss-seidel spectral radius is 0.9842851 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 00:27:24 rms-change max change #iterations 9.5719270E-02 16.13580 at 10iterations 7.3636491E-03 1.136538 at 20iterations 7.8339520E-04 0.1233330 at 30iterations 2.0095499E-04 4.2608261E-02 at 40iterations 7.0918824E-05 1.5127182E-02 at 50iterations finished qdiffx linear iterations at : 00:27:27 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.0918824E-05 1.5127182E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 00:27:27 3.414u 0.175s 0:03.90 91.7% 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 00:27:27 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 = 3383 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: 1.716462 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 1.716462 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.50004 assigned positive charge : 499.9665 centred at (gu) : 96.10681 87.47087 86.34462 assigned negative charge : -488.4682 centred at (gu) : 96.22391 86.92751 86.11144 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33413 grid for indexing accessible points = 1.400000 m= 27304 mr = 54899 m= 3250 mr = 18596 m= 136 mr = 1578 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.4000000 number of dielectric boundary points 38619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25116 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) : 0.5721541 object centre at (A) : 6.550502 50.24750 -0.4994993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3832966E-02 3.7435815E-02 midg,1,midg; midg,igrid,midg -1.9778395E-02 1.5242429E-02 1,midg,midg; igrid,midg,midg 7.9935677E-03 1.3777313E-02 gauss-seidel spectral radius is 0.9984200 estimated iterations to convergence 200 setup time was (sec) 0.6100000 now iterating at: 00:27:28 rms-change max change #iterations 3.917471 174.9571 at 10iterations 1.718049 64.09758 at 20iterations 0.7560290 25.07722 at 30iterations 0.3329166 10.35530 at 40iterations 0.1476769 4.551617 at 50iterations 6.5051213E-02 2.239803 at 60iterations 2.8742861E-02 0.9752636 at 70iterations 1.2806274E-02 0.4196625 at 80iterations 5.7376041E-03 0.1807575 at 90iterations 2.6157352E-03 8.4312439E-02 at 100iterations 1.2392550E-03 5.1159382E-02 at 110iterations 6.3331443E-04 2.2442818E-02 at 120iterations finished qdiffx linear iterations at : 00:27:35 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 6.3331443E-04 2.2442818E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 00:27:35 7.822u 0.211s 0:08.38 95.8% 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 00:27:36 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 = 3383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.574693 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): -24.56000 37.66100 ymin,ymax (A): 20.23600 80.25900 zmin,zma (A): -29.82500 28.82600 x,y,z range (A): 62.22100 60.02299 58.65100 scale (grids/A): 2.574693 object centre (A): 6.550502 50.24750 -0.4994993 number of atom coordinates read : 3383 total number of charged atoms : 3238 net assigned charge : 11.50004 assigned positive charge : 499.9665 centred at (gu) : 99.15982 86.20606 84.51664 assigned negative charge : -488.4682 centred at (gu) : 99.33589 85.39126 84.16704 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 192481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33413 grid for indexing accessible points = 1.400000 m= 91641 mr = 134633 m= 28438 mr = 71560 m= 5204 mr = 21376 m= 480 mr = 3271 m= 13 mr = 223 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 960 time to turn everything in is 1.020000 number of dielectric boundary points 87194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 25892 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) : 1.716462 object centre at (A) : 6.550502 50.24750 -0.4994993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3643723 0.5735441 midg,1,midg; midg,igrid,midg -0.1729902 0.1918831 1,midg,midg; igrid,midg,midg 2.8090378E-02 0.1132273 gauss-seidel spectral radius is 0.9992253 estimated iterations to convergence 284 setup time was (sec) 1.270000 now iterating at: 00:27:37 rms-change max change #iterations 10.00518 252.7929 at 10iterations 5.874730 126.6508 at 20iterations 3.409977 88.44353 at 30iterations 1.972858 46.98546 at 40iterations 1.133435 23.11423 at 50iterations 0.6493634 12.14924 at 60iterations 0.3711845 7.286280 at 70iterations 0.2122532 3.961706 at 80iterations 0.1207398 2.437282 at 90iterations 6.8910278E-02 1.156378 at 100iterations 3.9251927E-02 0.7170029 at 110iterations 2.2335146E-02 0.4069557 at 120iterations 1.2703531E-02 0.2270470 at 130iterations 7.2805397E-03 0.1528854 at 140iterations 4.1881143E-03 7.6631546E-02 at 150iterations 2.4230739E-03 4.6569824E-02 at 160iterations 1.4363538E-03 2.8084755E-02 at 170iterations 8.8018656E-04 2.1400452E-02 at 180iterations finished qdiffx linear iterations at : 00:27:49 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 8.8018656E-04 2.1400452E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 00:27:49 13.097u 0.208s 0:13.57 97.9% 0+0k 0+0io 0pf+0w