Sun Oct 9 00:04:12 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 00:04:12 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5665722 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 0.5665722 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 492.3325 centred at (gu) : 89.63139 89.80289 90.93569 assigned negative charge : -479.6082 centred at (gu) : 89.48984 89.83730 91.12019 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7325 nv = 96 ne = 84 npr = 64351 no. pairs analyzed = 64351 no. exposed pairs = 4444 no. arc points = 32234 no. surface atoms = 1468 nbur = 1860 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 = 1.512000 m= 354 mr = 3729 m= 3 mr = 8 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 0.2300000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3229 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9276 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5862107E-09 -1.3761127E-09 midg,1,midg; midg,igrid,midg 2.3880777E-09 1.1902705E-09 1,midg,midg; igrid,midg,midg -4.4824960E-10 3.5341081E-09 gauss-seidel spectral radius is 0.9839707 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 00:04:12 rms-change max change #iterations 9.6842356E-02 22.60387 at 10iterations 7.0109251E-03 1.090694 at 20iterations 5.2273227E-04 7.6881409E-02 at 30iterations 4.3858887E-05 7.6117516E-03 at 40iterations 4.6116002E-06 4.8065186E-04 at 50iterations finished qdiffx linear iterations at : 00:04:15 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 4.6116002E-06 4.8065186E-04 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 00:04:16 3.687u 0.218s 0:04.26 91.3% 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 Sun Oct 9 2011 at 00:04:16 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.699717 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 1.699717 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 492.3325 centred at (gu) : 88.89312 89.40768 92.80612 assigned negative charge : -479.6082 centred at (gu) : 88.46947 89.51147 93.36034 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32234 grid for indexing accessible points = 1.400000 m= 25805 mr = 53397 m= 2960 mr = 17671 m= 105 mr = 1536 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 0.3900000 number of dielectric boundary points 36648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24638 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) : 0.5665722 object centre at (A) : -24.25100 -18.17600 56.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7157377E-02 1.7115405E-02 midg,1,midg; midg,igrid,midg 4.2184111E-02 3.2581456E-02 1,midg,midg; igrid,midg,midg -9.1766445E-03 1.4999152E-02 gauss-seidel spectral radius is 0.9983847 estimated iterations to convergence 197 setup time was (sec) 0.6300000 now iterating at: 00:04:17 rms-change max change #iterations 3.832408 169.9985 at 10iterations 1.663493 59.92376 at 20iterations 0.7269758 23.96555 at 30iterations 0.3162826 10.24702 at 40iterations 0.1385694 4.380205 at 50iterations 6.0738202E-02 2.091328 at 60iterations 2.6532002E-02 0.8435793 at 70iterations 1.1596993E-02 0.3770390 at 80iterations 5.0623412E-03 0.1716982 at 90iterations 2.2251469E-03 7.5120926E-02 at 100iterations 9.7596837E-04 3.3041000E-02 at 110iterations 4.2668916E-04 1.4098644E-02 at 120iterations finished qdiffx linear iterations at : 00:04:24 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 4.2668916E-04 1.4098644E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 00:04:25 8.273u 0.260s 0:08.87 96.1% 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 Sun Oct 9 2011 at 00:04:25 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.549575 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 2.549575 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 492.3325 centred at (gu) : 88.33956 89.11133 94.20890 assigned negative charge : -479.6082 centred at (gu) : 87.70415 89.26715 95.04053 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 186126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32234 grid for indexing accessible points = 1.400000 m= 86964 mr = 130509 m= 26969 mr = 68381 m= 4917 mr = 20394 m= 451 mr = 3288 m= 14 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 3861 time to turn everything in is 0.9700000 number of dielectric boundary points 82638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 25424 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) : 1.699717 object centre at (A) : -24.25100 -18.17600 56.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7498589 0.2826681 midg,1,midg; midg,igrid,midg 0.7558985 0.6311844 1,midg,midg; igrid,midg,midg -8.6803578E-02 0.1978181 gauss-seidel spectral radius is 0.9992196 estimated iterations to convergence 283 setup time was (sec) 1.230000 now iterating at: 00:04:26 rms-change max change #iterations 9.764063 302.4736 at 10iterations 5.686715 136.9399 at 20iterations 3.286364 77.55584 at 30iterations 1.891135 44.74735 at 40iterations 1.084089 21.94723 at 50iterations 0.6178694 13.50218 at 60iterations 0.3523521 7.513762 at 70iterations 0.2006881 4.568350 at 80iterations 0.1138837 2.464546 at 90iterations 6.4608693E-02 1.277945 at 100iterations 3.6786821E-02 0.7184486 at 110iterations 2.0745449E-02 0.4007019 at 120iterations 1.1738200E-02 0.2194061 at 130iterations 6.6621131E-03 0.1432714 at 140iterations 3.7599034E-03 6.8243027E-02 at 150iterations 2.1291191E-03 3.8703918E-02 at 160iterations 1.2055261E-03 2.3418427E-02 at 170iterations 6.8218337E-04 1.3675690E-02 at 180iterations finished qdiffx linear iterations at : 00:04:38 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 6.8218337E-04 1.3675690E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 00:04:39 13.498u 0.233s 0:14.00 98.0% 0+0k 0+0io 0pf+0w