Sat Oct 8 15:14:50 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 Sat Oct 8 2011 at 15:14:50 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6325178 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 0.6325178 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.499999 assigned positive charge : 234.1845 centred at (gu) : 90.51682 90.04148 88.15321 assigned negative charge : -229.6843 centred at (gu) : 90.59734 90.02811 88.05737 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4440 nv = 96 ne = 84 npr = 29959 no. pairs analyzed = 29959 no. exposed pairs = 2108 no. arc points = 15100 no. surface atoms = 719 nbur = 861 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 224 mr = 2262 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1218771E-10 7.2273951E-09 midg,1,midg; midg,igrid,midg 4.6054933E-09 6.1941123E-09 1,midg,midg; igrid,midg,midg 8.8275494E-09 9.1650965E-10 gauss-seidel spectral radius is 0.9869682 estimated iterations to convergence 72 setup time was (sec) 0.4400000 now iterating at: 15:14:50 rms-change max change #iterations 0.1065065 18.13253 at 10iterations 1.0103860E-02 1.855354 at 20iterations 9.6003764E-04 0.1703329 at 30iterations 9.0972419E-05 1.6426086E-02 at 40iterations 8.4939238E-06 1.6345978E-03 at 50iterations finished qdiffx linear iterations at : 15:14:53 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 8.4939238E-06 1.6345978E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 15:14:54 3.198u 0.177s 0:03.68 91.3% 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 Sat Oct 8 2011 at 15:14:54 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897553 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 1.897553 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.499999 assigned positive charge : 234.1845 centred at (gu) : 91.55090 90.12489 84.45982 assigned negative charge : -229.6843 centred at (gu) : 91.79229 90.08461 84.17222 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 47692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15100 grid for indexing accessible points = 1.400000 m= 16050 mr = 31502 m= 2333 mr = 11424 m= 153 mr = 1317 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 21930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 11896 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) : 0.6325178 object centre at (A) : -32.78150 -8.817000 20.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2790404E-02 1.0543373E-02 midg,1,midg; midg,igrid,midg 2.3820230E-03 1.1050504E-02 1,midg,midg; igrid,midg,midg 3.3013534E-02 1.6856570E-02 gauss-seidel spectral radius is 0.9985213 estimated iterations to convergence 206 setup time was (sec) 0.6500000 now iterating at: 15:14:54 rms-change max change #iterations 3.161338 185.5389 at 10iterations 1.431366 55.58311 at 20iterations 0.6514428 28.09145 at 30iterations 0.2963633 12.44038 at 40iterations 0.1338249 4.806304 at 50iterations 6.0765490E-02 2.642313 at 60iterations 2.7642479E-02 1.024907 at 70iterations 1.2484394E-02 0.4853802 at 80iterations 5.6418944E-03 0.2357559 at 90iterations 2.5659604E-03 0.1032791 at 100iterations 1.1655474E-03 5.2576065E-02 at 110iterations 5.2725256E-04 2.1614075E-02 at 120iterations finished qdiffx linear iterations at : 15:15:01 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 5.2725256E-04 2.1614075E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 15:15:01 7.351u 0.209s 0:07.85 96.1% 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 15:15:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.846330 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 2.846330 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.499999 assigned positive charge : 234.1845 centred at (gu) : 92.32633 90.18748 81.68983 assigned negative charge : -229.6843 centred at (gu) : 92.68848 90.12700 81.25832 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 110148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15100 grid for indexing accessible points = 1.400000 m= 53107 mr = 76788 m= 18057 mr = 42456 m= 4025 mr = 13996 m= 570 mr = 2880 m= 51 mr = 344 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 49468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 12111 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) : 1.897553 object centre at (A) : -32.78150 -8.817000 20.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1911940 0.1013086 midg,1,midg; midg,igrid,midg 1.0304501E-02 0.1360658 1,midg,midg; igrid,midg,midg 0.3267356 6.9184519E-02 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.140000 now iterating at: 15:15:03 rms-change max change #iterations 7.498997 375.5400 at 10iterations 4.287398 127.5492 at 20iterations 2.441169 63.60244 at 30iterations 1.391115 34.47925 at 40iterations 0.7859632 18.19983 at 50iterations 0.4458376 11.00352 at 60iterations 0.2516907 6.609312 at 70iterations 0.1425225 3.125302 at 80iterations 8.0487728E-02 1.813156 at 90iterations 4.5273434E-02 1.026682 at 100iterations 2.5528582E-02 0.6003351 at 110iterations 1.4380403E-02 0.3330669 at 120iterations 8.1031909E-03 0.1795836 at 130iterations 4.5604804E-03 9.6553802E-02 at 140iterations 2.5605902E-03 6.7292333E-02 at 150iterations 1.4416114E-03 3.5113335E-02 at 160iterations 8.1518298E-04 2.1441460E-02 at 170iterations 4.5743518E-04 1.0754824E-02 at 180iterations finished qdiffx linear iterations at : 15:15:13 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 4.5743518E-04 1.0754824E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 15:15:14 11.722u 0.228s 0:12.31 96.9% 0+0k 0+0io 0pf+0w