Mon Oct 10 14:02:11 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 14:02:11 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 = 2785 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: 0.5387817 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 0.5387817 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.000019 assigned positive charge : 405.5300 centred at (gu) : 88.18188 89.35339 87.48695 assigned negative charge : -397.5304 centred at (gu) : 88.09530 89.30853 87.32306 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5413 nv = 96 ne = 84 npr = 54029 no. pairs analyzed = 54029 no. exposed pairs = 4104 no. arc points = 30162 no. surface atoms = 1361 nbur = 1424 mkacc time = 0.1200000 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 = 1.568000 m= 235 mr = 2365 m= 1 mr = 2 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 0.3200000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2941 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7017 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8375861E-10 5.9985006E-10 midg,1,midg; midg,igrid,midg 2.3201022E-10 5.1096760E-10 1,midg,midg; igrid,midg,midg 3.8061568E-12 4.9964588E-10 gauss-seidel spectral radius is 0.9822457 estimated iterations to convergence 62 setup time was (sec) 0.5500000 now iterating at: 14:02:12 rms-change max change #iterations 6.4148538E-02 12.08828 at 10iterations 4.0727146E-03 0.8631077 at 20iterations 2.6079995E-04 5.6407928E-02 at 30iterations 2.2660251E-05 3.2329559E-03 at 40iterations 3.6266542E-06 4.6157837E-04 at 50iterations finished qdiffx linear iterations at : 14:02:14 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.6266542E-06 4.6157837E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:02:15 3.360u 0.186s 0:04.25 83.2% 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 14:02:16 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 = 2785 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: 1.616345 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 1.616345 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.000019 assigned positive charge : 405.5300 centred at (gu) : 84.54516 88.05934 82.46049 assigned negative charge : -397.5304 centred at (gu) : 84.28552 87.92551 81.96863 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 58356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17513 mr = 35489 m= 1788 mr = 10969 m= 55 mr = 723 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 30531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20156 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) : 0.5387817 object centre at (A) : -10.13650 139.0185 180.9860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5011854E-03 7.0094294E-03 midg,1,midg; midg,igrid,midg 1.1449919E-02 1.6099028E-02 1,midg,midg; igrid,midg,midg -1.8358706E-02 -4.4593788E-03 gauss-seidel spectral radius is 0.9981405 estimated iterations to convergence 184 setup time was (sec) 0.7500000 now iterating at: 14:02:17 rms-change max change #iterations 3.032155 181.3325 at 10iterations 1.241239 56.70402 at 20iterations 0.5084738 17.95986 at 30iterations 0.2092860 8.424220 at 40iterations 8.6027957E-02 3.520475 at 50iterations 3.5232875E-02 1.561701 at 60iterations 1.4487175E-02 0.5214069 at 70iterations 5.9540542E-03 0.2289109 at 80iterations 2.4557456E-03 0.1067200 at 90iterations 1.0130282E-03 4.1778564E-02 at 100iterations 4.1670204E-04 1.6144753E-02 at 110iterations 1.7213046E-04 6.0405731E-03 at 120iterations finished qdiffx linear iterations at : 14:02:23 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.7213046E-04 6.0405731E-03 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 14:02:25 7.372u 0.235s 0:08.56 88.7% 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 14:02:25 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 = 2785 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: 2.424518 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 2.424518 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.000019 assigned positive charge : 405.5300 centred at (gu) : 81.81767 87.08907 78.69042 assigned negative charge : -397.5304 centred at (gu) : 81.42825 86.88834 77.95289 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 135260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59070 mr = 88044 m= 17249 mr = 43781 m= 2633 mr = 12082 m= 151 mr = 1492 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 68921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21060 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) : 1.616345 object centre at (A) : -10.13650 139.0185 180.9860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6256283E-02 9.0807214E-02 midg,1,midg; midg,igrid,midg 0.1610614 0.3050931 1,midg,midg; igrid,midg,midg -0.7311361 -0.1417190 gauss-seidel spectral radius is 0.9991275 estimated iterations to convergence 267 setup time was (sec) 1.310000 now iterating at: 14:02:26 rms-change max change #iterations 8.228385 391.6631 at 10iterations 4.693535 161.4499 at 20iterations 2.637411 82.43999 at 30iterations 1.476088 38.90336 at 40iterations 0.8197268 26.16810 at 50iterations 0.4553045 11.42070 at 60iterations 0.2517951 6.602479 at 70iterations 0.1390928 3.136395 at 80iterations 7.6259039E-02 2.034742 at 90iterations 4.2049427E-02 1.681940 at 100iterations 2.3084655E-02 0.6069336 at 110iterations 1.2666251E-02 0.3129387 at 120iterations 6.9624786E-03 0.1769466 at 130iterations 3.8156062E-03 8.3101273E-02 at 140iterations 2.0862513E-03 4.8358589E-02 at 150iterations 1.1465736E-03 2.8222978E-02 at 160iterations 6.2663783E-04 1.4914513E-02 at 170iterations 3.4334176E-04 8.8500977E-03 at 180iterations finished qdiffx linear iterations at : 14:02:36 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 3.4334176E-04 8.8500977E-03 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 14:02:37 11.629u 0.235s 0:12.50 94.8% 0+0k 0+0io 0pf+0w