Tue Oct 11 03:17:57 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 Tue Oct 11 2011 at 03:17:57 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2654 !!! WARNING: HIR 190 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: 0.6465909 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): 31.71500 86.77299 ymin,ymax (A): -22.56700 28.75200 zmin,zma (A): 2.051000 53.25000 x,y,z range (A): 55.05800 51.31900 51.19900 scale (grids/A): 0.6465909 object centre (A): 59.24400 3.092501 27.65050 number of atom coordinates read : 2654 total number of charged atoms : 2525 net assigned charge : 5.514005 assigned positive charge : 397.8926 centred at (gu) : 89.34126 90.30301 91.37695 assigned negative charge : -392.3795 centred at (gu) : 89.37086 90.16935 91.48507 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7587 nv = 96 ne = 84 npr = 52386 no. pairs analyzed = 52386 no. exposed pairs = 4061 no. arc points = 29247 no. surface atoms = 1314 nbur = 1340 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 3481 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2715 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8605911E-08 -7.7133517E-09 midg,1,midg; midg,igrid,midg -8.6161629E-09 3.0221720E-08 1,midg,midg; igrid,midg,midg 1.6029436E-08 4.9681503E-09 gauss-seidel spectral radius is 0.9876284 estimated iterations to convergence 73 setup time was (sec) 0.6500000 now iterating at: 03:17:58 rms-change max change #iterations 0.1539455 23.21059 at 10iterations 1.5395802E-02 2.321054 at 20iterations 1.6292324E-03 0.2367973 at 30iterations 2.4089865E-04 4.0884018E-02 at 40iterations 6.9084621E-05 1.3228416E-02 at 50iterations finished qdiffx linear iterations at : 03:18:02 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 6.9084621E-05 1.3228416E-02 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 03:18:02 4.600u 0.360s 0:05.27 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 Tue Oct 11 2011 at 03:18:02 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2654 !!! WARNING: HIR 190 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: 1.939773 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): 31.71500 86.77299 ymin,ymax (A): -22.56700 28.75200 zmin,zma (A): 2.051000 53.25000 x,y,z range (A): 55.05800 51.31900 51.19900 scale (grids/A): 1.939773 object centre (A): 59.24400 3.092501 27.65050 number of atom coordinates read : 2654 total number of charged atoms : 2525 net assigned charge : 5.514005 assigned positive charge : 397.8926 centred at (gu) : 88.02332 90.90855 94.13028 assigned negative charge : -392.3795 centred at (gu) : 88.11236 90.50791 94.45493 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29247 grid for indexing accessible points = 1.400000 m= 28994 mr = 49636 m= 5331 mr = 19243 m= 380 mr = 2930 m= 8 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.6600000 number of dielectric boundary points 42163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 19893 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) : 0.6465909 object centre at (A) : 59.24400 3.092501 27.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5351835E-02 5.9661963E-03 midg,1,midg; midg,igrid,midg -5.1356178E-02 3.0431250E-02 1,midg,midg; igrid,midg,midg 3.4312993E-02 7.4830125E-03 gauss-seidel spectral radius is 0.9987234 estimated iterations to convergence 222 setup time was (sec) 1.020000 now iterating at: 03:18:04 rms-change max change #iterations 4.519542 209.6604 at 10iterations 2.178131 78.20524 at 20iterations 1.048677 37.71218 at 30iterations 0.5038940 15.20626 at 40iterations 0.2433078 8.076933 at 50iterations 0.1167594 3.600614 at 60iterations 5.6025501E-02 1.874894 at 70iterations 2.7082562E-02 0.9286423 at 80iterations 1.2997729E-02 0.4403229 at 90iterations 6.3032373E-03 0.1896648 at 100iterations 3.0634585E-03 9.7000122E-02 at 110iterations 1.5157264E-03 5.0991774E-02 at 120iterations finished qdiffx linear iterations at : 03:18:14 total time elapsed so far: 11.12000 # loops : 120 mean,max change (kT/e) : 1.5157264E-03 5.0991774E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 03:18:14 11.290u 0.453s 0:12.04 97.5% 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 03:18:14 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2654 !!! WARNING: HIR 190 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: 2.909659 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): 31.71500 86.77299 ymin,ymax (A): -22.56700 28.75200 zmin,zma (A): 2.051000 53.25000 x,y,z range (A): 55.05800 51.31900 51.19900 scale (grids/A): 2.909659 object centre (A): 59.24400 3.092501 27.65050 number of atom coordinates read : 2654 total number of charged atoms : 2525 net assigned charge : 5.514005 assigned positive charge : 397.8926 centred at (gu) : 87.03490 91.36256 96.19527 assigned negative charge : -392.3795 centred at (gu) : 87.16848 90.76184 96.68233 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 182751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29247 grid for indexing accessible points = 1.400000 m= 89302 mr = 121636 m= 35102 mr = 68011 m= 9280 mr = 26159 m= 1575 mr = 6323 m= 118 mr = 951 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 1.800000 number of dielectric boundary points 95004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 20199 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) : 1.939773 object centre at (A) : 59.24400 3.092501 27.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3336975 5.7386197E-02 midg,1,midg; midg,igrid,midg -0.7547205 0.3679775 1,midg,midg; igrid,midg,midg 0.4431415 8.8796571E-02 gauss-seidel spectral radius is 0.9993188 estimated iterations to convergence 302 setup time was (sec) 2.160000 now iterating at: 03:18:17 rms-change max change #iterations 10.96252 506.8682 at 10iterations 6.759163 160.4317 at 20iterations 4.123687 91.77827 at 30iterations 2.490407 56.14290 at 40iterations 1.497462 35.02606 at 50iterations 0.8960543 18.93771 at 60iterations 0.5341003 10.86623 at 70iterations 0.3180414 5.999855 at 80iterations 0.1886513 4.002710 at 90iterations 0.1116890 2.011851 at 100iterations 6.6196606E-02 1.215685 at 110iterations 3.9047491E-02 0.7415848 at 120iterations 2.3028634E-02 0.4168035 at 130iterations 1.3604703E-02 0.2469766 at 140iterations 8.0216043E-03 0.1476498 at 150iterations 4.7298451E-03 8.7245464E-02 at 160iterations 2.7832862E-03 5.3660393E-02 at 170iterations 1.6440537E-03 2.8246403E-02 at 180iterations finished qdiffx linear iterations at : 03:18:34 total time elapsed so far: 19.10000 # loops : 180 mean,max change (kT/e) : 1.6440537E-03 2.8246403E-02 energy calculations done at 19.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.27000 DelPhi exited at 03:18:34 19.275u 0.454s 0:20.00 98.6% 0+0k 0+0io 0pf+0w