Sat Oct 15 14:37:56 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 Sat Oct 15 2011 at 14:38:00 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5920506 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 0.5920506 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.985964 assigned positive charge : 440.1519 centred at (gu) : 90.89286 89.52889 90.98029 assigned negative charge : -443.1392 centred at (gu) : 90.99907 89.41052 91.04153 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6910 nv = 96 ne = 84 npr = 57099 no. pairs analyzed = 57099 no. exposed pairs = 3845 no. arc points = 27955 no. surface atoms = 1296 nbur = 1603 mkacc time = 0.1500000 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= 331 mr = 3530 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3200000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2845 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4195434E-10 -3.6373726E-09 midg,1,midg; midg,igrid,midg -5.3423124E-09 2.5757583E-09 1,midg,midg; igrid,midg,midg 2.0200583E-09 -5.3968048E-09 gauss-seidel spectral radius is 0.9852754 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 14:38:02 rms-change max change #iterations 0.1063628 16.20451 at 10iterations 8.7739648E-03 1.241821 at 20iterations 7.2379509E-04 0.1147346 at 30iterations 5.9087386E-05 8.4981918E-03 at 40iterations 4.9383443E-06 8.7261200E-04 at 50iterations finished qdiffx linear iterations at : 14:38:09 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 4.9383443E-06 8.7261200E-04 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 14:38:10 4.054u 0.427s 0:10.91 40.9% 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 14:38:11 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.776152 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 1.776152 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.985964 assigned positive charge : 440.1519 centred at (gu) : 92.67770 88.58585 92.94024 assigned negative charge : -443.1392 centred at (gu) : 92.99670 88.23111 93.12441 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27955 grid for indexing accessible points = 1.400000 m= 24930 mr = 49923 m= 3128 mr = 17468 m= 143 mr = 1592 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 346 time to turn everything in is 0.6000000 number of dielectric boundary points 34257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21460 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) : 0.5920506 object centre at (A) : 2.599500 16.25550 33.79500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9478777E-02 1.6591709E-02 midg,1,midg; midg,igrid,midg -1.6287783E-02 5.4427073E-03 1,midg,midg; igrid,midg,midg 2.5204610E-02 -5.2691340E-02 gauss-seidel spectral radius is 0.9984771 estimated iterations to convergence 203 setup time was (sec) 0.8900000 now iterating at: 14:38:13 rms-change max change #iterations 4.026452 199.4848 at 10iterations 1.784104 61.32361 at 20iterations 0.7983211 26.93812 at 30iterations 0.3571579 11.82901 at 40iterations 0.1607692 5.544796 at 50iterations 7.1579657E-02 2.514671 at 60iterations 3.2170970E-02 1.171000 at 70iterations 1.4345409E-02 0.4751587 at 80iterations 6.4734467E-03 0.2164097 at 90iterations 2.8995944E-03 0.1081619 at 100iterations 1.2978557E-03 4.3011129E-02 at 110iterations 5.8261864E-04 2.1567106E-02 at 120iterations finished qdiffx linear iterations at : 14:38:31 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 5.8261864E-04 2.1567106E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 14:38:32 9.733u 0.510s 0:21.69 47.2% 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 14:38:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2899 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.664227 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): -27.26100 32.46000 ymin,ymax (A): -7.544000 40.05500 zmin,zma (A): 3.730000 63.86000 x,y,z range (A): 59.72100 47.59900 60.13000 scale (grids/A): 2.664227 object centre (A): 2.599500 16.25550 33.79500 number of atom coordinates read : 2899 total number of charged atoms : 2758 net assigned charge : -2.985964 assigned positive charge : 440.1519 centred at (gu) : 94.01638 87.87872 94.41023 assigned negative charge : -443.1392 centred at (gu) : 94.49500 87.34649 94.68661 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 173861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27955 grid for indexing accessible points = 1.400000 m= 83000 mr = 122256 m= 26977 mr = 65820 m= 5227 mr = 20675 m= 543 mr = 3399 m= 26 mr = 315 m= 0 mr = 3 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.510000 number of dielectric boundary points 77166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22061 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) : 1.776152 object centre at (A) : 2.599500 16.25550 33.79500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4915961 0.3320159 midg,1,midg; midg,igrid,midg -0.1804025 7.2238870E-02 1,midg,midg; igrid,midg,midg 0.4050515 -0.6647102 gauss-seidel spectral radius is 0.9992359 estimated iterations to convergence 286 setup time was (sec) 1.850000 now iterating at: 14:38:39 rms-change max change #iterations 9.912881 316.0827 at 10iterations 5.816633 158.2498 at 20iterations 3.371796 119.5343 at 30iterations 1.949630 43.08180 at 40iterations 1.120847 21.82677 at 50iterations 0.6435755 13.69492 at 60iterations 0.3685700 8.022713 at 70iterations 0.2107801 4.485503 at 80iterations 0.1204322 2.495726 at 90iterations 6.8774924E-02 1.285675 at 100iterations 3.9131328E-02 0.7337189 at 110iterations 2.2311896E-02 0.4619904 at 120iterations 1.2715062E-02 0.2321672 at 130iterations 7.2439266E-03 0.1440449 at 140iterations 4.1268156E-03 8.2351685E-02 at 150iterations 2.3480940E-03 4.4399075E-02 at 160iterations 1.3336890E-03 2.3861170E-02 at 170iterations 7.6082227E-04 1.3952255E-02 at 180iterations finished qdiffx linear iterations at : 14:39:08 total time elapsed so far: 17.04000 # loops : 180 mean,max change (kT/e) : 7.6082227E-04 1.3952255E-02 energy calculations done at 17.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.20000 DelPhi exited at 14:39:09 17.207u 0.536s 0:35.39 50.0% 0+0k 0+0io 0pf+0w