Sat Oct 15 13:45:44 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 15 2011 at 13:45:44 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 0.6113687 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 0.6113687 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 453.4871 centred at (gu) : 90.13329 89.04064 90.65538 assigned negative charge : -456.4879 centred at (gu) : 90.05208 88.92252 90.49074 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7212 nv = 96 ne = 84 npr = 58466 no. pairs analyzed = 58466 no. exposed pairs = 3572 no. arc points = 25683 no. surface atoms = 1194 nbur = 1723 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3988 m= 0 mr = 44 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3500000 number of dielectric boundary points 3562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2564 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0354801E-08 9.2560866E-09 midg,1,midg; midg,igrid,midg -1.1295246E-08 4.1920214E-09 1,midg,midg; igrid,midg,midg -6.6005374E-09 3.1370613E-09 gauss-seidel spectral radius is 0.9861745 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 13:45:45 rms-change max change #iterations 0.1293078 19.67849 at 10iterations 1.1801766E-02 1.721462 at 20iterations 1.1395586E-03 0.1678371 at 30iterations 1.8345707E-04 3.5594940E-02 at 40iterations 5.4455431E-05 1.1281967E-02 at 50iterations finished qdiffx linear iterations at : 13:45:49 total time elapsed so far: 5.140000 # loops : 50 mean,max change (kT/e) : 5.4455431E-05 1.1281967E-02 energy calculations done at 5.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.320000 DelPhi exited at 13:45:50 5.324u 0.449s 0:06.19 93.0% 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 15 2011 at 13:45:50 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 1.834106 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 1.834106 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 453.4871 centred at (gu) : 90.39886 87.12131 91.96571 assigned negative charge : -456.4879 centred at (gu) : 90.15574 86.76730 91.47173 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25683 grid for indexing accessible points = 1.400000 m= 27751 mr = 55167 m= 4089 mr = 20246 m= 191 mr = 2472 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1185 time to turn everything in is 0.6800000 number of dielectric boundary points 32928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21645 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) : 0.6113687 object centre at (A) : -1.115499 3.236001 -5.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2285165E-02 8.1908386E-03 midg,1,midg; midg,igrid,midg -5.7061438E-02 2.3623874E-02 1,midg,midg; igrid,midg,midg 2.4954514E-03 -2.6371346E-03 gauss-seidel spectral radius is 0.9985617 estimated iterations to convergence 209 setup time was (sec) 1.040000 now iterating at: 13:45:52 rms-change max change #iterations 4.322299 176.7581 at 10iterations 1.971102 63.92772 at 20iterations 0.9123608 28.08453 at 30iterations 0.4183023 14.46797 at 40iterations 0.1928670 5.811100 at 50iterations 8.8645577E-02 2.644911 at 60iterations 4.0679570E-02 1.280615 at 70iterations 1.8685021E-02 0.5367856 at 80iterations 8.5990047E-03 0.2838402 at 90iterations 3.9887549E-03 0.1186037 at 100iterations 1.8676429E-03 5.8588028E-02 at 110iterations 8.9082401E-04 2.8287888E-02 at 120iterations finished qdiffx linear iterations at : 13:46:03 total time elapsed so far: 12.48000 # loops : 120 mean,max change (kT/e) : 8.9082401E-04 2.8287888E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 13:46:04 12.649u 0.494s 0:13.44 97.6% 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 15 2011 at 13:46:04 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 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: 2.751159 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): -27.74800 25.51700 ymin,ymax (A): -25.87900 32.35100 zmin,zma (A): -29.66400 17.96700 x,y,z range (A): 53.26500 58.23000 47.63100 scale (grids/A): 2.751159 object centre (A): -1.115499 3.236001 -5.848500 number of atom coordinates read : 2917 total number of charged atoms : 2768 net assigned charge : -2.999975 assigned positive charge : 453.4871 centred at (gu) : 90.59824 85.68178 92.94836 assigned negative charge : -456.4879 centred at (gu) : 90.23351 85.15079 92.20743 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 182393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25683 grid for indexing accessible points = 1.400000 m= 90521 mr = 133302 m= 31868 mr = 73940 m= 7112 mr = 25388 m= 847 mr = 5263 m= 53 mr = 534 m= 0 mr = 23 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3872 time to turn everything in is 1.740000 number of dielectric boundary points 74344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 22140 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) : 1.834106 object centre at (A) : -1.115499 3.236001 -5.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9802880E-02 -1.0571333E-02 midg,1,midg; midg,igrid,midg -0.9417129 0.3642900 1,midg,midg; igrid,midg,midg 7.0584975E-02 -7.7352032E-02 gauss-seidel spectral radius is 0.9992456 estimated iterations to convergence 287 setup time was (sec) 2.190000 now iterating at: 13:46:06 rms-change max change #iterations 10.34147 379.3430 at 10iterations 6.058150 135.8448 at 20iterations 3.527029 65.11815 at 30iterations 2.042257 45.33871 at 40iterations 1.178029 25.81680 at 50iterations 0.6795310 13.11689 at 60iterations 0.3903842 7.508262 at 70iterations 0.2243433 4.941357 at 80iterations 0.1287737 2.455867 at 90iterations 7.3789977E-02 1.429775 at 100iterations 4.2295307E-02 0.8412037 at 110iterations 2.4221402E-02 0.4828682 at 120iterations 1.3885124E-02 0.2379513 at 130iterations 7.9440363E-03 0.1376921 at 140iterations 4.5506181E-03 8.2644463E-02 at 150iterations 2.6013467E-03 4.7906876E-02 at 160iterations 1.4893407E-03 3.2077789E-02 at 170iterations 8.5223559E-04 1.4287949E-02 at 180iterations finished qdiffx linear iterations at : 13:46:26 total time elapsed so far: 21.63000 # loops : 180 mean,max change (kT/e) : 8.5223559E-04 1.4287949E-02 energy calculations done at 21.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.79000 DelPhi exited at 13:46:26 21.798u 0.547s 0:22.68 98.4% 0+0k 0+0io 0pf+0w