Sat Oct 15 12:38:09 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 15 2011 at 12:38:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3178 !!! WARNING: NDP 1030 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5623924 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): 7.749000 54.58700 ymin,ymax (A): -31.13300 32.16800 zmin,zma (A): 121.6960 175.8830 x,y,z range (A): 46.83800 63.30100 54.18700 scale (grids/A): 0.5623924 object centre (A): 31.16800 0.5174990 148.7895 number of atom coordinates read : 3178 total number of charged atoms : 3040 net assigned charge : 10.00004 assigned positive charge : 474.7912 centred at (gu) : 90.58340 89.91226 89.59142 assigned negative charge : -464.7922 centred at (gu) : 90.63676 89.84778 89.61132 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6571 nv = 96 ne = 84 npr = 64701 no. pairs analyzed = 64701 no. exposed pairs = 3766 no. arc points = 26771 no. surface atoms = 1248 nbur = 1930 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 = 1.512000 m= 279 mr = 3612 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2300000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2651 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5607824E-09 8.3334800E-10 midg,1,midg; midg,igrid,midg 3.5353148E-10 1.9329587E-09 1,midg,midg; igrid,midg,midg 1.5985474E-09 5.5582161E-10 gauss-seidel spectral radius is 0.9837037 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 12:38:10 rms-change max change #iterations 8.7531723E-02 13.57943 at 10iterations 6.5192725E-03 0.9713583 at 20iterations 5.8844738E-04 9.1437310E-02 at 30iterations 1.1787493E-04 1.6962051E-02 at 40iterations 3.4956975E-05 4.9536228E-03 at 50iterations finished qdiffx linear iterations at : 12:38:16 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 3.4956975E-05 4.9536228E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 12:38:17 3.934u 0.228s 0:08.18 50.7% 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 Sat Oct 15 2011 at 12:38:17 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3178 !!! WARNING: NDP 1030 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.687177 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): 7.749000 54.58700 ymin,ymax (A): -31.13300 32.16800 zmin,zma (A): 121.6960 175.8830 x,y,z range (A): 46.83800 63.30100 54.18700 scale (grids/A): 1.687177 object centre (A): 31.16800 0.5174990 148.7895 number of atom coordinates read : 3178 total number of charged atoms : 3040 net assigned charge : 10.00004 assigned positive charge : 474.7912 centred at (gu) : 91.74960 89.73615 88.77332 assigned negative charge : -464.7922 centred at (gu) : 91.90997 89.54298 88.83362 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26771 grid for indexing accessible points = 1.400000 m= 24392 mr = 51087 m= 2798 mr = 17472 m= 96 mr = 1505 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2700 time to turn everything in is 0.3700000 number of dielectric boundary points 29907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23497 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) : 0.5623924 object centre at (A) : 31.16800 0.5174990 148.7895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0541875E-03 4.9692290E-03 midg,1,midg; midg,igrid,midg 1.8222746E-02 2.2678860E-02 1,midg,midg; igrid,midg,midg 6.9949022E-03 7.3032230E-03 gauss-seidel spectral radius is 0.9983236 estimated iterations to convergence 194 setup time was (sec) 0.6300000 now iterating at: 12:38:18 rms-change max change #iterations 3.696300 160.7607 at 10iterations 1.591492 54.33351 at 20iterations 0.6855993 24.02461 at 30iterations 0.2965179 10.01009 at 40iterations 0.1285505 4.319882 at 50iterations 5.5586863E-02 2.416012 at 60iterations 2.4107615E-02 0.7206783 at 70iterations 1.0453458E-02 0.3459091 at 80iterations 4.5269462E-03 0.1550348 at 90iterations 1.9813157E-03 6.9153070E-02 at 100iterations 8.8316860E-04 3.6071777E-02 at 110iterations 4.0546356E-04 1.5158653E-02 at 120iterations finished qdiffx linear iterations at : 12:38:26 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 4.0546356E-04 1.5158653E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 12:38:27 8.988u 0.302s 0:09.63 96.3% 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 15 2011 at 12:38:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3178 !!! WARNING: NDP 1030 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.530766 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): 7.749000 54.58700 ymin,ymax (A): -31.13300 32.16800 zmin,zma (A): 121.6960 175.8830 x,y,z range (A): 46.83800 63.30100 54.18700 scale (grids/A): 2.530766 object centre (A): 31.16800 0.5174990 148.7895 number of atom coordinates read : 3178 total number of charged atoms : 3040 net assigned charge : 10.00004 assigned positive charge : 474.7912 centred at (gu) : 92.62417 89.60394 88.15981 assigned negative charge : -464.7922 centred at (gu) : 92.86481 89.31432 88.25034 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26771 grid for indexing accessible points = 1.400000 m= 81734 mr = 124100 m= 26161 mr = 66205 m= 4707 mr = 20493 m= 385 mr = 3281 m= 18 mr = 205 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 9079 time to turn everything in is 0.9400000 number of dielectric boundary points 67368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 24301 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) : 1.687177 object centre at (A) : 31.16800 0.5174990 148.7895 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3944367E-02 6.2365733E-02 midg,1,midg; midg,igrid,midg 6.6833191E-02 0.2678516 1,midg,midg; igrid,midg,midg 7.1299240E-02 0.1179791 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.240000 now iterating at: 12:38:28 rms-change max change #iterations 9.249741 276.4871 at 10iterations 5.299786 122.4137 at 20iterations 3.016507 73.75641 at 30iterations 1.707991 40.47123 at 40iterations 0.9650632 22.18505 at 50iterations 0.5451539 12.58598 at 60iterations 0.3075231 8.127182 at 70iterations 0.1724636 3.451042 at 80iterations 9.6842684E-02 2.002450 at 90iterations 5.4451343E-02 1.071947 at 100iterations 3.0533439E-02 0.6087217 at 110iterations 1.7099904E-02 0.3653183 at 120iterations 9.5737614E-03 0.1894102 at 130iterations 5.3710621E-03 0.1098499 at 140iterations 3.0049603E-03 6.1813354E-02 at 150iterations 1.6850241E-03 3.4656525E-02 at 160iterations 9.4362098E-04 1.8480301E-02 at 170iterations 5.2854395E-04 9.9167824E-03 at 180iterations finished qdiffx linear iterations at : 12:38:42 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 5.2854395E-04 9.9167824E-03 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 12:38:42 14.916u 0.300s 0:15.53 97.9% 0+0k 0+0io 0pf+0w