Sun Oct 9 14:12:55 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 14:12:55 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 = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5691447 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 0.5691447 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 9.000022 assigned positive charge : 408.9004 centred at (gu) : 89.61987 90.89815 88.56572 assigned negative charge : -399.9015 centred at (gu) : 89.57845 90.74236 88.64135 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5762 nv = 96 ne = 84 npr = 52856 no. pairs analyzed = 52856 no. exposed pairs = 3509 no. arc points = 24979 no. surface atoms = 1171 nbur = 1522 mkacc time = 8.9999996E-02 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= 253 mr = 2901 m= 0 mr = 8 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2565 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7318 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2729568E-09 1.9723706E-10 midg,1,midg; midg,igrid,midg -6.9115647E-10 4.2071808E-09 1,midg,midg; igrid,midg,midg 7.9532747E-10 1.7066304E-09 gauss-seidel spectral radius is 0.9840512 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 14:12:56 rms-change max change #iterations 8.3727524E-02 15.66293 at 10iterations 6.3305306E-03 0.9952650 at 20iterations 4.6993021E-04 7.1279526E-02 at 30iterations 3.7494345E-05 6.2198639E-03 at 40iterations 4.4011963E-06 7.3885918E-04 at 50iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.4011963E-06 7.3885918E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:12:59 3.397u 0.158s 0:03.83 92.4% 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 14:12:59 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 = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.707434 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 1.707434 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 9.000022 assigned positive charge : 408.9004 centred at (gu) : 88.85899 92.69398 85.69674 assigned negative charge : -399.9015 centred at (gu) : 88.73505 92.22693 85.92380 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24979 grid for indexing accessible points = 1.400000 m= 19963 mr = 41659 m= 2237 mr = 13524 m= 87 mr = 1088 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 28780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19736 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) : 0.5691447 object centre at (A) : 26.19100 14.44100 15.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0019521E-02 8.9329816E-03 midg,1,midg; midg,igrid,midg 1.2054987E-03 1.5794655E-02 1,midg,midg; igrid,midg,midg -1.1113384E-02 -1.9815653E-03 gauss-seidel spectral radius is 0.9983246 estimated iterations to convergence 194 setup time was (sec) 0.5300000 now iterating at: 14:13:00 rms-change max change #iterations 3.424789 161.0435 at 10iterations 1.472607 57.78111 at 20iterations 0.6375630 24.84406 at 30iterations 0.2747496 10.38218 at 40iterations 0.1182353 4.068218 at 50iterations 5.0954614E-02 1.958633 at 60iterations 2.1945363E-02 0.9168239 at 70iterations 9.4900513E-03 0.3273115 at 80iterations 4.1035819E-03 0.1447754 at 90iterations 1.7682969E-03 6.4634323E-02 at 100iterations 7.6308509E-04 2.4621964E-02 at 110iterations 3.3147691E-04 1.2420654E-02 at 120iterations finished qdiffx linear iterations at : 14:13:07 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.3147691E-04 1.2420654E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 14:13:07 7.700u 0.193s 0:08.18 96.4% 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 14:13:07 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 = 2693 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.561151 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): -7.0999980E-02 52.45300 ymin,ymax (A): -9.783999 38.66600 zmin,zma (A): -15.67100 46.87900 x,y,z range (A): 52.52400 48.45000 62.55000 scale (grids/A): 2.561151 object centre (A): 26.19100 14.44100 15.60400 number of atom coordinates read : 2693 total number of charged atoms : 2554 net assigned charge : 9.000022 assigned positive charge : 408.9004 centred at (gu) : 88.28833 94.04092 83.54485 assigned negative charge : -399.9015 centred at (gu) : 88.10248 93.34013 83.88562 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24979 grid for indexing accessible points = 1.400000 m= 67485 mr = 101763 m= 20140 mr = 52872 m= 3539 mr = 14917 m= 312 mr = 2232 m= 16 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 64967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20412 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) : 1.707434 object centre at (A) : 26.19100 14.44100 15.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.085384 0.1384561 midg,1,midg; midg,igrid,midg -4.6004541E-03 0.1504586 1,midg,midg; igrid,midg,midg -0.1410670 -5.9402984E-02 gauss-seidel spectral radius is 0.9991771 estimated iterations to convergence 275 setup time was (sec) 1.000000 now iterating at: 14:13:08 rms-change max change #iterations 8.787967 293.6017 at 10iterations 5.086400 134.6711 at 20iterations 2.915839 75.72414 at 30iterations 1.651463 38.26712 at 40iterations 0.9366174 24.33016 at 50iterations 0.5285584 12.51814 at 60iterations 0.2973393 6.420799 at 70iterations 0.1667729 3.869635 at 80iterations 9.3763329E-02 2.127074 at 90iterations 5.2561983E-02 1.169214 at 100iterations 2.9346585E-02 0.5919213 at 110iterations 1.6398780E-02 0.3518276 at 120iterations 9.1716042E-03 0.1795015 at 130iterations 5.1096473E-03 0.1111240 at 140iterations 2.8590136E-03 6.2507629E-02 at 150iterations 1.5930607E-03 3.7388325E-02 at 160iterations 8.8907470E-04 2.1392822E-02 at 170iterations 4.9602194E-04 1.1286736E-02 at 180iterations finished qdiffx linear iterations at : 14:13:20 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 4.9602194E-04 1.1286736E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 14:13:20 12.213u 0.211s 0:12.72 97.6% 0+0k 0+0io 0pf+0w