Tue Oct 11 03:16:06 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 Tue Oct 11 2011 at 03:16:06 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 = 3224 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: 0.5357815 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): 59.56300 110.5530 ymin,ymax (A): -3.182000 55.97400 zmin,zma (A): 35.76600 102.2110 x,y,z range (A): 50.99000 59.15600 66.44500 scale (grids/A): 0.5357815 object centre (A): 85.05800 26.39600 68.98849 number of atom coordinates read : 3224 total number of charged atoms : 3085 net assigned charge : -5.999974 assigned positive charge : 483.1607 centred at (gu) : 88.72186 91.76530 92.74232 assigned negative charge : -489.1618 centred at (gu) : 88.76165 91.75616 92.77254 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5874 nv = 96 ne = 84 npr = 65965 no. pairs analyzed = 65965 no. exposed pairs = 4048 no. arc points = 27971 no. surface atoms = 1372 nbur = 1852 mkacc time = 0.1700000 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 = 1.596000 m= 240 mr = 3065 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2881 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2550620E-11 -7.8419721E-10 midg,1,midg; midg,igrid,midg -1.8771715E-10 -3.0683736E-10 1,midg,midg; igrid,midg,midg -6.5679948E-11 -3.1984093E-10 gauss-seidel spectral radius is 0.9820607 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 03:16:07 rms-change max change #iterations 7.0445992E-02 11.30256 at 10iterations 4.4715721E-03 0.6700001 at 20iterations 3.5169916E-04 7.0884228E-02 at 30iterations 5.2461073E-05 1.1367947E-02 at 40iterations 1.1981327E-05 2.7619749E-03 at 50iterations finished qdiffx linear iterations at : 03:16:12 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 1.1981327E-05 2.7619749E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.180000 DelPhi exited at 03:16:12 5.180u 0.444s 0:05.96 94.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 03:16:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3224 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: 1.607344 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): 59.56300 110.5530 ymin,ymax (A): -3.182000 55.97400 zmin,zma (A): 35.76600 102.2110 x,y,z range (A): 50.99000 59.15600 66.44500 scale (grids/A): 1.607344 object centre (A): 85.05800 26.39600 68.98849 number of atom coordinates read : 3224 total number of charged atoms : 3085 net assigned charge : -5.999974 assigned positive charge : 483.1607 centred at (gu) : 86.16454 95.29529 98.22587 assigned negative charge : -489.1618 centred at (gu) : 86.28422 95.26783 98.31703 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20047 mr = 44310 m= 1998 mr = 13909 m= 59 mr = 986 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 561 time to turn everything in is 0.5800000 number of dielectric boundary points 28261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23482 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) : 0.5357815 object centre at (A) : 85.05800 26.39600 68.98849 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3812275E-02 -1.3658229E-02 midg,1,midg; midg,igrid,midg -4.0854118E-03 2.4059995E-03 1,midg,midg; igrid,midg,midg -3.2570243E-03 -5.6925965E-03 gauss-seidel spectral radius is 0.9981356 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 03:16:14 rms-change max change #iterations 3.361251 205.8004 at 10iterations 1.378382 58.49299 at 20iterations 0.5693930 21.57431 at 30iterations 0.2350945 8.287831 at 40iterations 9.7150140E-02 3.652656 at 50iterations 3.9930776E-02 1.418388 at 60iterations 1.6510768E-02 0.6004181 at 70iterations 6.7916727E-03 0.2587471 at 80iterations 2.8215286E-03 0.1057215 at 90iterations 1.1751241E-03 3.9367676E-02 at 100iterations 4.9571664E-04 1.9137383E-02 at 110iterations 2.1253615E-04 8.5036755E-03 at 120iterations finished qdiffx linear iterations at : 03:16:24 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 2.1253615E-04 8.5036755E-03 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 03:16:25 11.932u 0.502s 0:12.77 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 Tue Oct 11 2011 at 03:16:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3224 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: 2.411017 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): 59.56300 110.5530 ymin,ymax (A): -3.182000 55.97400 zmin,zma (A): 35.76600 102.2110 x,y,z range (A): 50.99000 59.15600 66.44500 scale (grids/A): 2.411017 object centre (A): 85.05800 26.39600 68.98849 number of atom coordinates read : 3224 total number of charged atoms : 3085 net assigned charge : -5.999974 assigned positive charge : 483.1607 centred at (gu) : 84.24645 97.94267 102.3385 assigned negative charge : -489.1618 centred at (gu) : 84.42628 97.90154 102.4754 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 151761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27971 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69814 mr = 108348 m= 19712 mr = 55391 m= 3111 mr = 14991 m= 222 mr = 2000 m= 8 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 1.390000 number of dielectric boundary points 63799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 24639 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) : 1.607344 object centre at (A) : 85.05800 26.39600 68.98849 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4389666 -0.3247599 midg,1,midg; midg,igrid,midg -3.5677556E-05 0.1620468 1,midg,midg; igrid,midg,midg -4.0439237E-02 -8.5922949E-02 gauss-seidel spectral radius is 0.9991243 estimated iterations to convergence 267 setup time was (sec) 1.770000 now iterating at: 03:16:27 rms-change max change #iterations 8.783128 320.9767 at 10iterations 4.909867 143.3667 at 20iterations 2.727791 65.08495 at 30iterations 1.506791 34.29012 at 40iterations 0.8298717 18.25403 at 50iterations 0.4571903 9.465759 at 60iterations 0.2510558 5.271536 at 70iterations 0.1376982 3.241720 at 80iterations 7.5439014E-02 1.581717 at 90iterations 4.1235067E-02 0.8697004 at 100iterations 2.2609118E-02 0.4563932 at 110iterations 1.2375444E-02 0.2665806 at 120iterations 6.7771743E-03 0.1392517 at 130iterations 3.7095537E-03 7.5290203E-02 at 140iterations 2.0357491E-03 4.1582108E-02 at 150iterations 1.1185516E-03 2.2079468E-02 at 160iterations 6.1770610E-04 1.3086557E-02 at 170iterations 3.4299717E-04 7.2870255E-03 at 180iterations finished qdiffx linear iterations at : 03:16:49 total time elapsed so far: 23.86000 # loops : 180 mean,max change (kT/e) : 3.4299717E-04 7.2870255E-03 energy calculations done at 23.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.03000 DelPhi exited at 03:16:50 24.033u 0.523s 0:24.87 98.7% 0+0k 0+0io 0pf+0w