Mon Oct 10 14:38:50 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 14:38:50 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5854108 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 0.5854108 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 419.6436 centred at (gu) : 92.06164 89.87829 89.61527 assigned negative charge : -423.2443 centred at (gu) : 91.98822 89.95953 89.67379 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6213 nv = 96 ne = 84 npr = 52093 no. pairs analyzed = 52093 no. exposed pairs = 3719 no. arc points = 26122 no. surface atoms = 1255 nbur = 1435 mkacc time = 0.1400000 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 = 1.456000 m= 318 mr = 3102 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2594 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0394572E-10 -2.2520281E-09 midg,1,midg; midg,igrid,midg 1.0440624E-09 -2.9529792E-09 1,midg,midg; igrid,midg,midg -1.7680228E-09 1.3834023E-09 gauss-seidel spectral radius is 0.9849196 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 14:38:51 rms-change max change #iterations 0.1018488 17.99469 at 10iterations 8.1022512E-03 1.310337 at 20iterations 6.4794143E-04 0.1080980 at 30iterations 5.4657656E-05 8.4896088E-03 at 40iterations 6.2756449E-06 1.0452271E-03 at 50iterations finished qdiffx linear iterations at : 14:38:56 total time elapsed so far: 5.010000 # loops : 50 mean,max change (kT/e) : 6.2756449E-06 1.0452271E-03 energy calculations done at 5.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 14:38:57 5.176u 0.431s 0:06.58 85.1% 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 Mon Oct 10 2011 at 14:38:57 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.756232 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 1.756232 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 419.6436 centred at (gu) : 96.18423 89.63425 88.84528 assigned negative charge : -423.2443 centred at (gu) : 95.96445 89.87850 89.02105 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26122 grid for indexing accessible points = 1.400000 m= 22497 mr = 44204 m= 3151 mr = 15261 m= 130 mr = 1631 m= 0 mr = 24 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19790 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) : 0.5854108 object centre at (A) : 22.31900 9.248500 104.1255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4558001E-03 -2.8552508E-02 midg,1,midg; midg,igrid,midg -5.2398294E-03 -1.5557849E-02 1,midg,midg; igrid,midg,midg 1.6276630E-02 3.4783248E-02 gauss-seidel spectral radius is 0.9984233 estimated iterations to convergence 200 setup time was (sec) 0.8700000 now iterating at: 14:38:58 rms-change max change #iterations 3.815539 158.3077 at 10iterations 1.679632 68.00409 at 20iterations 0.7434269 30.56995 at 30iterations 0.3289509 10.90042 at 40iterations 0.1454013 5.525410 at 50iterations 6.4227566E-02 2.147446 at 60iterations 2.8506430E-02 0.9964466 at 70iterations 1.2590349E-02 0.4513550 at 80iterations 5.5701500E-03 0.2101959 at 90iterations 2.4712768E-03 8.7951660E-02 at 100iterations 1.0966730E-03 3.5507202E-02 at 110iterations 4.8613854E-04 1.6677856E-02 at 120iterations finished qdiffx linear iterations at : 14:39:09 total time elapsed so far: 12.12000 # loops : 120 mean,max change (kT/e) : 4.8613854E-04 1.6677856E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:39:10 12.291u 0.443s 0:13.64 93.3% 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 Mon Oct 10 2011 at 14:39:10 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.634349 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 2.634349 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 419.6436 centred at (gu) : 99.27621 89.45129 88.26773 assigned negative charge : -423.2443 centred at (gu) : 98.94648 89.81767 88.53144 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 154889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26122 grid for indexing accessible points = 1.400000 m= 74119 mr = 108243 m= 24864 mr = 57713 m= 5132 mr = 18638 m= 595 mr = 3454 m= 21 mr = 336 m= 0 mr = 4 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 71232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20380 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) : 1.756232 object centre at (A) : 22.31900 9.248500 104.1255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1015725 -0.3908020 midg,1,midg; midg,igrid,midg -8.4961176E-02 -0.1705764 1,midg,midg; igrid,midg,midg 0.3535427 0.3975333 gauss-seidel spectral radius is 0.9992086 estimated iterations to convergence 281 setup time was (sec) 1.820000 now iterating at: 14:39:13 rms-change max change #iterations 9.480390 323.4580 at 10iterations 5.493732 171.6129 at 20iterations 3.151351 70.36430 at 30iterations 1.798845 38.25386 at 40iterations 1.023313 20.08897 at 50iterations 0.5830967 13.89197 at 60iterations 0.3303899 6.880817 at 70iterations 0.1870201 3.781315 at 80iterations 0.1056566 2.098253 at 90iterations 5.9680529E-02 1.202929 at 100iterations 3.3684831E-02 0.6289234 at 110iterations 1.9037459E-02 0.3584199 at 120iterations 1.0739839E-02 0.2364492 at 130iterations 6.0616899E-03 0.1380463 at 140iterations 3.4232948E-03 7.3242188E-02 at 150iterations 1.9315112E-03 3.8131714E-02 at 160iterations 1.0908255E-03 2.4239540E-02 at 170iterations 6.1699480E-04 1.2517452E-02 at 180iterations finished qdiffx linear iterations at : 14:39:30 total time elapsed so far: 18.82000 # loops : 180 mean,max change (kT/e) : 6.1699480E-04 1.2517452E-02 energy calculations done at 18.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.99000 DelPhi exited at 14:39:31 18.991u 0.509s 0:20.68 94.2% 0+0k 0+0io 0pf+0w