Tue Oct 11 07:38:14 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 Tue Oct 11 2011 at 07:38:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 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: 0.6990672 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 0.6990672 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2290 net assigned charge : 5.500006 assigned positive charge : 363.8562 centred at (gu) : 91.04193 88.55602 89.73795 assigned negative charge : -358.3567 centred at (gu) : 91.11295 88.53831 89.86393 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8066 nv = 96 ne = 84 npr = 49486 no. pairs analyzed = 49486 no. exposed pairs = 2866 no. arc points = 19723 no. surface atoms = 977 nbur = 1667 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4765 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1818 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9029 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0168966E-07 -2.0302942E-08 midg,1,midg; midg,igrid,midg 3.9316465E-08 3.5358347E-08 1,midg,midg; igrid,midg,midg 5.8243479E-08 5.2852651E-09 gauss-seidel spectral radius is 0.9893680 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 07:38:15 rms-change max change #iterations 0.2079232 30.58817 at 10iterations 2.5624305E-02 3.496822 at 20iterations 3.3774453E-03 0.4356728 at 30iterations 5.4899615E-04 8.3366394E-02 at 40iterations 1.1918624E-04 1.7673492E-02 at 50iterations finished qdiffx linear iterations at : 07:38:18 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1918624E-04 1.7673492E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:38:18 3.392u 0.199s 0:04.27 83.8% 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 Tue Oct 11 2011 at 07:38:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 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: 2.097202 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 2.097202 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2290 net assigned charge : 5.500006 assigned positive charge : 363.8562 centred at (gu) : 93.12537 85.66758 89.21335 assigned negative charge : -358.3567 centred at (gu) : 93.33865 85.61479 89.59163 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19723 grid for indexing accessible points = 1.400000 m= 34518 mr = 60988 m= 6732 mr = 26819 m= 549 mr = 4605 m= 12 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 34253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18178 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) : 0.6990672 object centre at (A) : 12.53450 1.658000 16.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7879866E-02 -9.0872087E-03 midg,1,midg; midg,igrid,midg 1.8754821E-02 2.2996405E-02 1,midg,midg; igrid,midg,midg 1.9119674E-02 1.9261880E-02 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.9100000 now iterating at: 07:38:20 rms-change max change #iterations 4.889556 230.5379 at 10iterations 2.429878 80.68608 at 20iterations 1.207439 32.73336 at 30iterations 0.6016453 17.53043 at 40iterations 0.2995794 8.886053 at 50iterations 0.1493793 4.160465 at 60iterations 7.4335285E-02 2.078610 at 70iterations 3.7056435E-02 1.072090 at 80iterations 1.8552108E-02 0.5185375 at 90iterations 9.3170833E-03 0.2755318 at 100iterations 4.7081588E-03 0.1397471 at 110iterations 2.3973945E-03 6.9263458E-02 at 120iterations finished qdiffx linear iterations at : 07:38:26 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.3973945E-03 6.9263458E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 07:38:27 7.860u 0.268s 0:08.66 93.7% 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 Tue Oct 11 2011 at 07:38:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 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: 3.145802 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): -12.92800 37.99700 ymin,ymax (A): -22.11800 25.43400 zmin,zma (A): -6.562000 40.03100 x,y,z range (A): 50.92500 47.55200 46.59300 scale (grids/A): 3.145802 object centre (A): 12.53450 1.658000 16.73450 number of atom coordinates read : 2644 total number of charged atoms : 2290 net assigned charge : 5.500006 assigned positive charge : 363.8562 centred at (gu) : 94.68783 83.50124 88.81990 assigned negative charge : -358.3567 centred at (gu) : 95.00797 83.42211 89.38738 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 196418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19723 grid for indexing accessible points = 1.400000 m= 107178 mr = 146715 m= 44264 mr = 90397 m= 12817 mr = 37054 m= 2373 mr = 10103 m= 237 mr = 1770 m= 8 mr = 157 m= 0 mr = 2 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 77097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 18318 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) : 2.097202 object centre at (A) : 12.53450 1.658000 16.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7466833E-02 -0.1158316 midg,1,midg; midg,igrid,midg 0.1386463 0.1232802 1,midg,midg; igrid,midg,midg 2.4286756E-02 2.9727131E-02 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 2.260000 now iterating at: 07:38:30 rms-change max change #iterations 10.79845 421.6064 at 10iterations 6.341798 135.4500 at 20iterations 3.731081 74.15349 at 30iterations 2.191026 36.66045 at 40iterations 1.285990 26.56274 at 50iterations 0.7512290 12.22285 at 60iterations 0.4391314 8.307656 at 70iterations 0.2574218 4.392218 at 80iterations 0.1502443 2.479566 at 90iterations 8.7945938E-02 1.391201 at 100iterations 5.1598404E-02 0.8246536 at 110iterations 3.0236950E-02 0.4897308 at 120iterations 1.7849626E-02 0.3144264 at 130iterations 1.0636797E-02 0.1854248 at 140iterations 6.4453078E-03 0.1124344 at 150iterations 4.0135183E-03 7.2563171E-02 at 160iterations 2.6011644E-03 4.5085907E-02 at 170iterations 1.7738739E-03 3.1982422E-02 at 180iterations finished qdiffx linear iterations at : 07:38:41 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 1.7738739E-03 3.1982422E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 07:38:41 13.311u 0.279s 0:14.07 96.5% 0+0k 0+0io 0pf+0w