Sat Oct 8 19:00:38 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 Sat Oct 8 2011 at 19:00:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 0.6378556 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 0.6378556 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.67546 89.18884 90.31935 assigned negative charge : -388.8955 centred at (gu) : 88.56042 89.22528 90.20825 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 53933 no. pairs analyzed = 53933 no. exposed pairs = 3068 no. arc points = 22018 no. surface atoms = 1033 nbur = 1572 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 378 mr = 3972 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6640896E-09 1.9641000E-08 midg,1,midg; midg,igrid,midg 1.2193075E-08 1.9300819E-09 1,midg,midg; igrid,midg,midg -8.8967838E-09 1.4142158E-08 gauss-seidel spectral radius is 0.9872645 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 19:00:39 rms-change max change #iterations 0.1427899 20.65189 at 10iterations 1.4293621E-02 2.063022 at 20iterations 1.3936922E-03 0.1968842 at 30iterations 1.4075902E-04 1.7539978E-02 at 40iterations 1.3508045E-05 1.8959045E-03 at 50iterations finished qdiffx linear iterations at : 19:00:43 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.3508045E-05 1.8959045E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 19:00:43 4.373u 0.286s 0:04.94 94.1% 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 Sat Oct 8 2011 at 19:00:43 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 1.913567 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 1.913567 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 86.02573 87.56596 90.95757 assigned negative charge : -388.8955 centred at (gu) : 85.68116 87.67556 90.62425 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22018 grid for indexing accessible points = 1.400000 m= 27817 mr = 53511 m= 4437 mr = 20796 m= 252 mr = 2786 m= 1 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1542 time to turn everything in is 0.6300000 number of dielectric boundary points 31361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19438 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) : 0.6378556 object centre at (A) : -7.384501 -0.3074999 15.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6111610E-02 3.0902263E-02 midg,1,midg; midg,igrid,midg 1.5672570E-02 9.3315163E-04 1,midg,midg; igrid,midg,midg -7.4854684E-03 4.2363886E-02 gauss-seidel spectral radius is 0.9986473 estimated iterations to convergence 215 setup time was (sec) 0.9800000 now iterating at: 19:00:45 rms-change max change #iterations 4.273839 179.4584 at 10iterations 2.012790 70.79786 at 20iterations 0.9454100 31.72581 at 30iterations 0.4447680 16.14643 at 40iterations 0.2080088 6.600731 at 50iterations 9.7934365E-02 3.264557 at 60iterations 4.5990404E-02 1.626923 at 70iterations 2.1696100E-02 0.6890287 at 80iterations 1.0159302E-02 0.3155994 at 90iterations 4.7878209E-03 0.1579223 at 100iterations 2.2503510E-03 7.6068878E-02 at 110iterations 1.0598400E-03 3.4492493E-02 at 120iterations finished qdiffx linear iterations at : 19:00:54 total time elapsed so far: 9.790000 # loops : 120 mean,max change (kT/e) : 1.0598400E-03 3.4492493E-02 energy calculations done at 9.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.970000 DelPhi exited at 19:00:54 9.977u 0.327s 0:10.57 97.3% 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 Sat Oct 8 2011 at 19:00:54 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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: 2.870350 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): -32.29800 17.52900 ymin,ymax (A): -23.68000 23.06500 zmin,zma (A): -12.64800 43.16400 x,y,z range (A): 49.82700 46.74500 55.81200 scale (grids/A): 2.870350 object centre (A): -7.384501 -0.3074999 15.25800 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.03849 86.34879 91.43618 assigned negative charge : -388.8955 centred at (gu) : 83.52176 86.51325 90.93639 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 175991 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22018 grid for indexing accessible points = 1.400000 m= 89966 mr = 129208 m= 32393 mr = 74544 m= 7846 mr = 26202 m= 1173 mr = 5908 m= 94 mr = 766 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 4990 time to turn everything in is 1.510000 number of dielectric boundary points 70785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19728 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) : 1.913567 object centre at (A) : -7.384501 -0.3074999 15.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3139185E-02 0.4518528 midg,1,midg; midg,igrid,midg 0.1809444 -3.7632667E-02 1,midg,midg; igrid,midg,midg -2.5323462E-02 0.4670935 gauss-seidel spectral radius is 0.9992562 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 19:00:56 rms-change max change #iterations 9.893419 348.4258 at 10iterations 5.706804 118.5042 at 20iterations 3.276239 68.88480 at 30iterations 1.882513 34.28212 at 40iterations 1.082444 19.40143 at 50iterations 0.6210491 11.19006 at 60iterations 0.3564095 6.075607 at 70iterations 0.2043867 3.770689 at 80iterations 0.1173370 2.070051 at 90iterations 6.7191660E-02 1.165798 at 100iterations 3.8518138E-02 0.7002230 at 110iterations 2.2065269E-02 0.4067650 at 120iterations 1.2618545E-02 0.2222557 at 130iterations 7.2499216E-03 0.1310656 at 140iterations 4.1593411E-03 7.3025703E-02 at 150iterations 2.3866382E-03 4.2370319E-02 at 160iterations 1.3652275E-03 2.5188684E-02 at 170iterations 7.8378938E-04 1.3889313E-02 at 180iterations finished qdiffx linear iterations at : 19:01:11 total time elapsed so far: 16.22000 # loops : 180 mean,max change (kT/e) : 7.8378938E-04 1.3889313E-02 energy calculations done at 16.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 19:01:11 16.396u 0.346s 0:17.01 98.3% 0+0k 0+0io 0pf+0w