Mon Oct 10 10:25:00 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 Mon Oct 10 2011 at 10:25:00 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 = 2567 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5825179 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 0.5825179 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.000019 assigned positive charge : 375.0974 centred at (gu) : 88.60073 88.70673 87.40614 assigned negative charge : -366.0977 centred at (gu) : 88.60645 88.58649 87.37165 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6054 nv = 96 ne = 84 npr = 48812 no. pairs analyzed = 48812 no. exposed pairs = 4076 no. arc points = 29583 no. surface atoms = 1327 nbur = 1240 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 = 1.484000 m= 307 mr = 2588 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6815747E-09 1.5841413E-09 midg,1,midg; midg,igrid,midg -3.1504035E-10 3.3255168E-09 1,midg,midg; igrid,midg,midg 3.1437510E-09 1.5080865E-09 gauss-seidel spectral radius is 0.9847754 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 10:25:00 rms-change max change #iterations 9.0591855E-02 13.79016 at 10iterations 7.0036929E-03 1.198871 at 20iterations 5.6552421E-04 9.2273712E-02 at 30iterations 4.6592319E-05 8.1205368E-03 at 40iterations 5.3064491E-06 8.6975098E-04 at 50iterations finished qdiffx linear iterations at : 10:25:03 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.3064491E-06 8.6975098E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 10:25:04 3.499u 0.188s 0:04.01 91.5% 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 Mon Oct 10 2011 at 10:25:04 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 = 2567 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.747554 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 1.747554 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.000019 assigned positive charge : 375.0974 centred at (gu) : 85.80181 86.12000 82.21812 assigned negative charge : -366.0977 centred at (gu) : 85.81934 85.75941 82.11484 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29583 grid for indexing accessible points = 1.400000 m= 20569 mr = 38591 m= 2738 mr = 12735 m= 132 mr = 1148 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 35065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18812 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) : 0.5825179 object centre at (A) : 6.732500 -32.00050 30.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9342307E-02 6.3502355E-03 midg,1,midg; midg,igrid,midg 2.6006280E-02 3.0194331E-02 1,midg,midg; igrid,midg,midg 7.6785390E-03 9.1541447E-03 gauss-seidel spectral radius is 0.9984052 estimated iterations to convergence 199 setup time was (sec) 0.8600000 now iterating at: 10:25:05 rms-change max change #iterations 3.489432 168.2159 at 10iterations 1.530726 57.53161 at 20iterations 0.6699050 27.21305 at 30iterations 0.2941982 11.53279 at 40iterations 0.1295423 4.691364 at 50iterations 5.6773033E-02 1.960482 at 60iterations 2.4899691E-02 0.8693943 at 70iterations 1.0939534E-02 0.4407291 at 80iterations 4.8050061E-03 0.1643524 at 90iterations 2.1107341E-03 7.8477383E-02 at 100iterations 9.3066588E-04 3.3977509E-02 at 110iterations 4.0903327E-04 1.5291214E-02 at 120iterations finished qdiffx linear iterations at : 10:25:12 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.0903327E-04 1.5291214E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 10:25:12 8.057u 0.182s 0:08.54 96.3% 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 Mon Oct 10 2011 at 10:25:12 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 = 2567 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: 2.621331 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 2.621331 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.000019 assigned positive charge : 375.0974 centred at (gu) : 83.70266 84.17986 78.32719 assigned negative charge : -366.0977 centred at (gu) : 83.72901 83.63913 78.17211 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 147922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29583 grid for indexing accessible points = 1.400000 m= 67063 mr = 95322 m= 22164 mr = 49157 m= 4463 mr = 15505 m= 387 mr = 2560 m= 21 mr = 167 m= 0 mr = 4 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 79305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 19382 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) : 1.747554 object centre at (A) : 6.732500 -32.00050 30.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1546878 5.4977428E-02 midg,1,midg; midg,igrid,midg 0.4286671 0.4053251 1,midg,midg; igrid,midg,midg 6.1335284E-03 8.8266730E-02 gauss-seidel spectral radius is 0.9992190 estimated iterations to convergence 282 setup time was (sec) 1.620000 now iterating at: 10:25:14 rms-change max change #iterations 8.921326 299.8529 at 10iterations 5.265633 161.8123 at 20iterations 3.080225 75.39047 at 30iterations 1.785118 47.07112 at 40iterations 1.028874 25.37062 at 50iterations 0.5879791 16.49731 at 60iterations 0.3373990 7.992125 at 70iterations 0.1921086 5.095139 at 80iterations 0.1095796 2.558580 at 90iterations 6.2167257E-02 1.390554 at 100iterations 3.5322987E-02 0.8292847 at 110iterations 1.9985646E-02 0.4132671 at 120iterations 1.1352465E-02 0.2445793 at 130iterations 6.4062886E-03 0.1362419 at 140iterations 3.6376473E-03 7.9205990E-02 at 150iterations 2.0602483E-03 4.3670654E-02 at 160iterations 1.1625161E-03 2.4517059E-02 at 170iterations 6.5710139E-04 1.4205933E-02 at 180iterations finished qdiffx linear iterations at : 10:25:26 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 6.5710139E-04 1.4205933E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 10:25:26 13.328u 0.265s 0:14.04 96.7% 0+0k 0+0io 0pf+0w