Sun Oct 9 08:34:15 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 Sun Oct 9 2011 at 08:34:15 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5540 !!! WARNING: HIR 702 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5264794 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 0.5264794 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.485979 assigned positive charge : 833.3050 centred at (gu) : 89.29662 88.49213 89.61591 assigned negative charge : -838.7979 centred at (gu) : 89.37231 88.50330 89.47872 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9749 nv = 96 ne = 84 npr = 112353 no. pairs analyzed = 112353 no. exposed pairs = 6836 no. arc points = 47447 no. surface atoms = 2306 nbur = 3234 mkacc time = 0.3200000 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 = 1.624000 m= 402 mr = 5172 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.6200000 number of dielectric boundary points 4955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4693 ## 641 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 13047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0763838E-09 5.7487826E-10 midg,1,midg; midg,igrid,midg -1.2886880E-10 -1.5132143E-10 1,midg,midg; igrid,midg,midg 3.4384595E-10 -5.0388932E-10 gauss-seidel spectral radius is 0.9816008 estimated iterations to convergence 61 setup time was (sec) 0.9000000 now iterating at: 08:34:16 rms-change max change #iterations 8.5264355E-02 11.95923 at 10iterations 5.7018893E-03 0.7902770 at 20iterations 6.0837949E-04 0.1309967 at 30iterations 1.5600708E-04 3.6670685E-02 at 40iterations 4.9026537E-05 1.0944366E-02 at 50iterations finished qdiffx linear iterations at : 08:34:19 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 4.9026537E-05 1.0944366E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 08:34:20 4.403u 0.284s 0:05.24 89.3% 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 Sun Oct 9 2011 at 08:34:20 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5540 !!! WARNING: HIR 702 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.579438 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 1.579438 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.485979 assigned positive charge : 833.3050 centred at (gu) : 87.88805 85.47459 88.84578 assigned negative charge : -838.7979 centred at (gu) : 88.11687 85.50976 88.43593 start vw surface at 0.2400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 109286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32906 mr = 75629 m= 3385 mr = 22260 m= 90 mr = 1649 m= 0 mr = 5 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.9600000 number of dielectric boundary points 46124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 627 ## 10 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 40843 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) : 0.5264794 object centre at (A) : 35.98050 57.22250 94.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9091293E-02 1.0305264E-02 midg,1,midg; midg,igrid,midg -1.3588645E-02 -1.1771674E-02 1,midg,midg; igrid,midg,midg 6.4044450E-03 2.6131370E-03 gauss-seidel spectral radius is 0.9983069 estimated iterations to convergence 193 setup time was (sec) 1.280000 now iterating at: 08:34:22 rms-change max change #iterations 4.433734 166.5912 at 10iterations 1.902177 62.80038 at 20iterations 0.8186183 26.40610 at 30iterations 0.3514095 10.27882 at 40iterations 0.1513401 4.343470 at 50iterations 6.5018222E-02 2.202004 at 60iterations 2.8020963E-02 0.8015260 at 70iterations 1.2061144E-02 0.3280048 at 80iterations 5.2298126E-03 0.1498304 at 90iterations 2.2874638E-03 6.6789627E-02 at 100iterations 1.0056685E-03 2.8762817E-02 at 110iterations 4.5536051E-04 1.5604019E-02 at 120iterations finished qdiffx linear iterations at : 08:34:31 total time elapsed so far: 10.01000 # loops : 120 mean,max change (kT/e) : 4.5536051E-04 1.5604019E-02 energy calculations done at 10.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.19000 DelPhi exited at 08:34:31 10.188u 0.316s 0:10.80 97.1% 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 Sun Oct 9 2011 at 08:34:31 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5540 !!! WARNING: HIR 702 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.369157 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): 3.370000 68.59100 ymin,ymax (A): 24.86900 89.57600 zmin,zma (A): 60.29300 127.9120 x,y,z range (A): 65.22100 64.70700 67.61899 scale (grids/A): 2.369157 object centre (A): 35.98050 57.22250 94.10250 number of atom coordinates read : 5540 total number of charged atoms : 5374 net assigned charge : -5.485979 assigned positive charge : 833.3050 centred at (gu) : 86.83195 83.21138 88.26830 assigned negative charge : -838.7979 centred at (gu) : 87.17516 83.26451 87.65374 start vw surface at 0.2400000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 254262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47447 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 116137 mr = 185305 m= 31735 mr = 91121 m= 5215 mr = 23627 m= 346 mr = 3519 m= 6 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 1.470000 no. cavity mid-points inaccessible to solvent = 2166 time to turn everything in is 2.390000 number of dielectric boundary points 103986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 2.560000 number of grid points assigned charge 42919 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) : 1.579438 object centre at (A) : 35.98050 57.22250 94.10250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5223185 9.0282507E-02 midg,1,midg; midg,igrid,midg -0.3668320 -0.1646025 1,midg,midg; igrid,midg,midg 0.2782409 0.2161459 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 2.740000 now iterating at: 08:34:34 rms-change max change #iterations 11.77740 311.4530 at 10iterations 6.962264 160.1031 at 20iterations 4.095982 84.83873 at 30iterations 2.399292 42.84498 at 40iterations 1.395602 27.13021 at 50iterations 0.8113457 14.63151 at 60iterations 0.4696176 8.638333 at 70iterations 0.2713474 4.618206 at 80iterations 0.1567054 2.604610 at 90iterations 9.0291381E-02 1.487913 at 100iterations 5.1941141E-02 0.8660011 at 110iterations 2.9868005E-02 0.5094695 at 120iterations 1.7162995E-02 0.2931890 at 130iterations 9.8681059E-03 0.1809120 at 140iterations 5.6742672E-03 9.5840454E-02 at 150iterations 3.2604991E-03 5.6663632E-02 at 160iterations 1.8797229E-03 3.1557083E-02 at 170iterations 1.0820058E-03 1.9449234E-02 at 180iterations finished qdiffx linear iterations at : 08:34:49 total time elapsed so far: 17.64000 # loops : 180 mean,max change (kT/e) : 1.0820058E-03 1.9449234E-02 energy calculations done at 17.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.83000 DelPhi exited at 08:34:50 17.827u 0.328s 0:18.45 98.3% 0+0k 0+0io 0pf+0w