Wed Dec 21 14:20:51 PST 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 Wed Dec 21 2011 at 14:20:51 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: 231 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6058234 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 0.6058234 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 284.1861 centred at (gu) : 89.63005 90.15275 90.47110 assigned negative charge : -281.5053 centred at (gu) : 89.62738 90.29153 90.65772 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4878 nv = 96 ne = 84 npr = 39016 no. pairs analyzed = 39016 no. exposed pairs = 2534 no. arc points = 17601 no. surface atoms = 858 nbur = 1075 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 245 mr = 2626 m= 0 mr = 18 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1821 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 5907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4869972E-09 -5.1354911E-09 midg,1,midg; midg,igrid,midg 5.5621516E-09 -3.1385687E-09 1,midg,midg; igrid,midg,midg 1.4635265E-09 1.4015179E-09 gauss-seidel spectral radius is 0.9858420 estimated iterations to convergence 69 setup time was (sec) 0.4900000 now iterating at: 14:20:52 rms-change max change #iterations 9.7689651E-02 18.08639 at 10iterations 8.3783325E-03 1.310501 at 20iterations 7.0957158E-04 0.1195221 at 30iterations 6.1622995E-05 1.0112762E-02 at 40iterations 5.3297495E-06 8.6593628E-04 at 50iterations finished qdiffx linear iterations at : 14:20:55 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 5.3297495E-06 8.6593628E-04 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 14:20:56 3.982u 0.360s 0:04.62 93.9% 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 Wed Dec 21 2011 at 14:20:56 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: 231 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.817470 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 1.817470 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 284.1861 centred at (gu) : 88.89019 90.45812 91.41341 assigned negative charge : -281.5053 centred at (gu) : 88.88234 90.87471 91.97313 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 52631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17601 grid for indexing accessible points = 1.400000 m= 19169 mr = 35853 m= 2707 mr = 14194 m= 89 mr = 1625 m= 0 mr = 21 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 22903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14092 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) : 0.6058234 object centre at (A) : 5.696502 0.8284998 17.55750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2467656E-03 -8.8392422E-03 midg,1,midg; midg,igrid,midg 6.9586067E-03 -4.4856099E-03 1,midg,midg; igrid,midg,midg 3.5715677E-02 3.6376044E-02 gauss-seidel spectral radius is 0.9984273 estimated iterations to convergence 200 setup time was (sec) 0.6800000 now iterating at: 14:20:57 rms-change max change #iterations 3.212012 146.9649 at 10iterations 1.418221 58.84767 at 20iterations 0.6280804 23.11152 at 30iterations 0.2771084 10.15629 at 40iterations 0.1229611 5.133881 at 50iterations 5.4275051E-02 1.984825 at 60iterations 2.4024822E-02 0.9549236 at 70iterations 1.0626176E-02 0.4500797 at 80iterations 4.7154888E-03 0.1807098 at 90iterations 2.0849062E-03 8.2216263E-02 at 100iterations 9.2534447E-04 3.4492493E-02 at 110iterations 4.0980027E-04 1.5725613E-02 at 120iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 4.0980027E-04 1.5725613E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 14:21:06 9.411u 0.447s 0:10.66 92.4% 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 Wed Dec 21 2011 at 14:21:07 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: 231 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.726205 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 2.726205 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 284.1861 centred at (gu) : 88.33524 90.68715 92.12015 assigned negative charge : -281.5053 centred at (gu) : 88.32347 91.31216 92.95987 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 121210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17601 grid for indexing accessible points = 1.400000 m= 62245 mr = 86627 m= 22031 mr = 50886 m= 4575 mr = 17688 m= 448 mr = 3376 m= 14 mr = 276 m= 0 mr = 3 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 51667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14393 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) : 1.817470 object centre at (A) : 5.696502 0.8284998 17.55750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5374305E-02 -6.5640718E-02 midg,1,midg; midg,igrid,midg 5.7281211E-02 -4.0514953E-02 1,midg,midg; igrid,midg,midg 0.4162842 0.5276558 gauss-seidel spectral radius is 0.9991860 estimated iterations to convergence 277 setup time was (sec) 1.210000 now iterating at: 14:21:08 rms-change max change #iterations 7.811318 290.9676 at 10iterations 4.441887 113.1050 at 20iterations 2.509868 61.16621 at 30iterations 1.411431 32.87256 at 40iterations 0.7944891 18.63896 at 50iterations 0.4479907 9.993567 at 60iterations 0.2502168 5.721112 at 70iterations 0.1403472 3.205809 at 80iterations 7.8568839E-02 1.730782 at 90iterations 4.3947145E-02 1.033325 at 100iterations 2.4569247E-02 0.5238876 at 110iterations 1.3720780E-02 0.2904949 at 120iterations 7.6928283E-03 0.1618905 at 130iterations 4.3064458E-03 9.8852158E-02 at 140iterations 2.3956378E-03 5.3169250E-02 at 150iterations 1.3389087E-03 2.9150963E-02 at 160iterations 7.4733671E-04 1.6016006E-02 at 170iterations 4.1855985E-04 9.0112686E-03 at 180iterations finished qdiffx linear iterations at : 14:21:22 total time elapsed so far: 14.55000 # loops : 180 mean,max change (kT/e) : 4.1855985E-04 9.0112686E-03 energy calculations done at 14.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.68000 DelPhi exited at 14:21:32 14.686u 0.500s 0:25.55 59.4% 0+0k 0+0io 0pf+0w