Sat Oct 8 14:32:27 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 Sat Oct 8 2011 at 14:32:27 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3047 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6149594 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 0.6149594 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.014007 assigned positive charge : 458.6576 centred at (gu) : 91.50433 91.80888 91.11034 assigned negative charge : -457.6443 centred at (gu) : 91.52776 91.74508 91.18050 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7435 nv = 96 ne = 84 npr = 64543 no. pairs analyzed = 64543 no. exposed pairs = 3526 no. arc points = 24120 no. surface atoms = 1202 nbur = 1845 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 4273 m= 2 mr = 30 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 3484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2417 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1893329E-09 -5.2290652E-09 midg,1,midg; midg,igrid,midg -2.4035505E-09 7.4574071E-09 1,midg,midg; igrid,midg,midg 1.6243040E-09 -1.2604179E-09 gauss-seidel spectral radius is 0.9863368 estimated iterations to convergence 70 setup time was (sec) 0.6500000 now iterating at: 14:32:28 rms-change max change #iterations 0.1346438 18.87732 at 10iterations 1.2587582E-02 1.755392 at 20iterations 1.2577836E-03 0.1748915 at 30iterations 1.5443472E-04 2.2363663E-02 at 40iterations 2.6259826E-05 4.0550232E-03 at 50iterations finished qdiffx linear iterations at : 14:32:32 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 2.6259826E-05 4.0550232E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 14:32:32 4.653u 0.410s 0:05.32 95.1% 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 14:32:32 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3047 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.844878 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 1.844878 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.014007 assigned positive charge : 458.6576 centred at (gu) : 94.51241 95.42619 93.33050 assigned negative charge : -457.6443 centred at (gu) : 94.58304 95.23492 93.54097 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24120 grid for indexing accessible points = 1.400000 m= 28514 mr = 59083 m= 3868 mr = 21172 m= 178 mr = 2259 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 32229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22726 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) : 0.6149594 object centre at (A) : 10.89750 16.36600 -13.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3961823E-02 7.7470220E-03 midg,1,midg; midg,igrid,midg -1.9539215E-02 4.2032961E-02 1,midg,midg; igrid,midg,midg 6.7145899E-03 -5.3501362E-03 gauss-seidel spectral radius is 0.9985792 estimated iterations to convergence 210 setup time was (sec) 1.020000 now iterating at: 14:32:34 rms-change max change #iterations 4.371698 165.9995 at 10iterations 2.023563 63.72832 at 20iterations 0.9376439 29.94960 at 30iterations 0.4332649 13.16704 at 40iterations 0.2000602 6.348742 at 50iterations 9.2470713E-02 2.835464 at 60iterations 4.2795908E-02 1.359957 at 70iterations 1.9801650E-02 0.6078835 at 80iterations 9.1380253E-03 0.2750320 at 90iterations 4.2308806E-03 0.1351767 at 100iterations 1.9611625E-03 5.8409214E-02 at 110iterations 9.0741587E-04 2.6253700E-02 at 120iterations finished qdiffx linear iterations at : 14:32:43 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 9.0741587E-04 2.6253700E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 14:32:44 10.700u 0.429s 0:11.52 96.5% 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 Sat Oct 8 2011 at 14:32:44 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3047 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.767317 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): -13.92800 35.72300 ymin,ymax (A): -12.57900 45.31100 zmin,zma (A): -39.96400 12.52200 x,y,z range (A): 49.65100 57.89000 52.48600 scale (grids/A): 2.767317 object centre (A): 10.89750 16.36600 -13.72100 number of atom coordinates read : 3047 total number of charged atoms : 2900 net assigned charge : 1.014007 assigned positive charge : 458.6576 centred at (gu) : 96.76830 98.13892 94.99545 assigned negative charge : -457.6443 centred at (gu) : 96.87441 97.85223 95.31138 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 190884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24120 grid for indexing accessible points = 1.400000 m= 95544 mr = 143326 m= 31313 mr = 79093 m= 6624 mr = 24962 m= 701 mr = 4770 m= 19 mr = 378 m= 1 mr = 2 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 72556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 23197 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) : 1.844878 object centre at (A) : 10.89750 16.36600 -13.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1366426 0.2341049 midg,1,midg; midg,igrid,midg -0.1478340 0.6330116 1,midg,midg; igrid,midg,midg 0.1044137 -3.2432843E-02 gauss-seidel spectral radius is 0.9992466 estimated iterations to convergence 288 setup time was (sec) 2.080000 now iterating at: 14:32:47 rms-change max change #iterations 10.40969 372.8325 at 10iterations 6.071493 142.8505 at 20iterations 3.510462 72.82648 at 30iterations 2.022037 35.29820 at 40iterations 1.164728 22.87199 at 50iterations 0.6686141 12.64505 at 60iterations 0.3838554 6.890549 at 70iterations 0.2207642 3.832415 at 80iterations 0.1261385 2.299236 at 90iterations 7.2262488E-02 1.385191 at 100iterations 4.1417513E-02 0.6996384 at 110iterations 2.3694320E-02 0.4122057 at 120iterations 1.3598577E-02 0.2484169 at 130iterations 7.7897725E-03 0.1385727 at 140iterations 4.4606351E-03 8.5720062E-02 at 150iterations 2.5600304E-03 4.1283607E-02 at 160iterations 1.4674312E-03 2.6273727E-02 at 170iterations 8.4464182E-04 1.5335083E-02 at 180iterations finished qdiffx linear iterations at : 14:33:03 total time elapsed so far: 18.77000 # loops : 180 mean,max change (kT/e) : 8.4464182E-04 1.5335083E-02 energy calculations done at 18.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.95000 DelPhi exited at 14:33:04 18.951u 0.466s 0:19.69 98.5% 0+0k 0+0io 0pf+0w