Tue Oct 11 03:39:23 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 03:39:23 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 = 2730 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6641915 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 0.6641915 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5000139 assigned positive charge : 412.9488 centred at (gu) : 90.19613 90.33188 91.42838 assigned negative charge : -412.4493 centred at (gu) : 89.89698 90.14741 91.37398 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8079 nv = 96 ne = 84 npr = 55956 no. pairs analyzed = 55956 no. exposed pairs = 3268 no. arc points = 22690 no. surface atoms = 1091 nbur = 1639 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4696 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2186 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6668024E-09 1.8540218E-08 midg,1,midg; midg,igrid,midg -3.9968779E-08 4.6470415E-08 1,midg,midg; igrid,midg,midg -6.8177521E-08 7.1686195E-08 gauss-seidel spectral radius is 0.9882580 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 03:39:24 rms-change max change #iterations 0.1736339 24.89498 at 10iterations 1.9156650E-02 2.705948 at 20iterations 2.1164382E-03 0.3014832 at 30iterations 2.4954803E-04 3.2183647E-02 at 40iterations 3.9498784E-05 5.1002502E-03 at 50iterations finished qdiffx linear iterations at : 03:39:26 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.9498784E-05 5.1002502E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 03:39:27 3.143u 0.164s 0:03.86 85.4% 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 03:39:27 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 = 2730 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.992574 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 1.992574 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5000139 assigned positive charge : 412.9488 centred at (gu) : 90.58797 90.99508 94.28440 assigned negative charge : -412.4493 centred at (gu) : 89.69048 90.44193 94.12177 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22690 grid for indexing accessible points = 1.400000 m= 33985 mr = 62297 m= 5659 mr = 25865 m= 378 mr = 3696 m= 6 mr = 170 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 408 time to turn everything in is 0.6200000 number of dielectric boundary points 35031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20398 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) : 0.6641915 object centre at (A) : 12.59850 -2.582500 18.70950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0813520E-02 -8.4401434E-03 midg,1,midg; midg,igrid,midg -3.0372266E-02 3.3476111E-02 1,midg,midg; igrid,midg,midg -1.2976780E-02 8.0564693E-02 gauss-seidel spectral radius is 0.9987583 estimated iterations to convergence 225 setup time was (sec) 0.9100000 now iterating at: 03:39:28 rms-change max change #iterations 4.781339 216.6698 at 10iterations 2.332716 75.66595 at 20iterations 1.131313 39.12091 at 30iterations 0.5490699 17.39150 at 40iterations 0.2683941 7.304443 at 50iterations 0.1302018 3.823538 at 60iterations 6.3193351E-02 1.821011 at 70iterations 3.0730760E-02 0.9316053 at 80iterations 1.4913357E-02 0.4127645 at 90iterations 7.2792089E-03 0.2154503 at 100iterations 3.5500517E-03 0.1059076 at 110iterations 1.7462153E-03 4.7658920E-02 at 120iterations finished qdiffx linear iterations at : 03:39:36 total time elapsed so far: 8.670000 # loops : 120 mean,max change (kT/e) : 1.7462153E-03 4.7658920E-02 energy calculations done at 8.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.850000 DelPhi exited at 03:39:37 8.851u 0.243s 0:09.68 93.9% 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 Tue Oct 11 2011 at 03:39:37 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 = 2730 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: 2.988862 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): -12.00000 37.19700 ymin,ymax (A): -26.85500 21.69000 zmin,zma (A): -8.090000 45.50900 x,y,z range (A): 49.19700 48.54500 53.59900 scale (grids/A): 2.988862 object centre (A): 12.59850 -2.582500 18.70950 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 0.5000139 assigned positive charge : 412.9488 centred at (gu) : 90.88176 91.49266 96.42637 assigned negative charge : -412.4493 centred at (gu) : 89.53571 90.66286 96.18260 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 200576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22690 grid for indexing accessible points = 1.400000 m= 107795 mr = 149723 m= 41678 mr = 90044 m= 10261 mr = 34195 m= 1639 mr = 7909 m= 152 mr = 1207 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 1431 time to turn everything in is 1.560000 number of dielectric boundary points 78949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 20655 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) : 1.992574 object centre at (A) : 12.59850 -2.582500 18.70950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9474171 0.1532045 midg,1,midg; midg,igrid,midg -0.3286976 0.4059953 1,midg,midg; igrid,midg,midg -0.1584827 0.6740340 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.870000 now iterating at: 03:39:39 rms-change max change #iterations 10.97779 396.8058 at 10iterations 6.475722 146.7934 at 20iterations 3.795098 74.31091 at 30iterations 2.223968 57.13161 at 40iterations 1.303759 24.25219 at 50iterations 0.7610447 13.69889 at 60iterations 0.4443420 7.640107 at 70iterations 0.2595683 4.676786 at 80iterations 0.1512886 2.406147 at 90iterations 8.8199869E-02 1.395123 at 100iterations 5.1421084E-02 0.8797150 at 110iterations 2.9922048E-02 0.4981792 at 120iterations 1.7429043E-02 0.3014717 at 130iterations 1.0169820E-02 0.1675272 at 140iterations 5.9402115E-03 0.1016598 at 150iterations 3.4763948E-03 5.7323456E-02 at 160iterations 2.0487728E-03 3.2894135E-02 at 170iterations 1.2153969E-03 2.0694733E-02 at 180iterations finished qdiffx linear iterations at : 03:39:50 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.2153969E-03 2.0694733E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 03:39:50 12.913u 0.269s 0:13.83 95.2% 0+0k 0+0io 0pf+0w