Sat Oct 8 18:27:33 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+sph2.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 = amb2.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 18:27:33 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5719243 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): 50.07200 108.7600 ymin,ymax (A): 10.30100 72.34800 zmin,zma (A): 38.43500 100.6810 x,y,z range (A): 58.68800 62.04700 62.24600 scale (grids/A): 0.5719243 object centre (A): 79.41600 41.32450 69.55800 number of atom coordinates read : 3526 total number of charged atoms : 3382 net assigned charge : 5.000020 assigned positive charge : 529.5370 centred at (gu) : 89.25698 89.82632 89.76719 assigned negative charge : -524.5386 centred at (gu) : 89.37271 89.71415 89.74177 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7717 nv = 96 ne = 84 npr = 69652 no. pairs analyzed = 69652 no. exposed pairs = 4804 no. arc points = 33901 no. surface atoms = 1595 nbur = 1931 mkacc time = 0.2400000 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= 332 mr = 3824 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3398 ## 356 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9836 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2123415E-10 1.2433856E-09 midg,1,midg; midg,igrid,midg -1.5048234E-09 2.8812706E-09 1,midg,midg; igrid,midg,midg 3.6693202E-09 -1.2598259E-09 gauss-seidel spectral radius is 0.9842792 estimated iterations to convergence 66 setup time was (sec) 0.8200000 now iterating at: 18:27:34 rms-change max change #iterations 0.1034015 17.92986 at 10iterations 8.2820123E-03 1.190223 at 20iterations 9.7955333E-04 0.1585159 at 30iterations 2.4044860E-04 3.4805298E-02 at 40iterations 7.1146795E-05 1.0353088E-02 at 50iterations finished qdiffx linear iterations at : 18:27:37 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 7.1146795E-05 1.0353088E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 18:27:38 4.619u 0.422s 0:05.57 90.3% 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 18:27:38 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.715773 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): 50.07200 108.7600 ymin,ymax (A): 10.30100 72.34800 zmin,zma (A): 38.43500 100.6810 x,y,z range (A): 58.68800 62.04700 62.24600 scale (grids/A): 1.715773 object centre (A): 79.41600 41.32450 69.55800 number of atom coordinates read : 3526 total number of charged atoms : 3382 net assigned charge : 5.000020 assigned positive charge : 529.5370 centred at (gu) : 87.76939 89.47807 89.30054 assigned negative charge : -524.5386 centred at (gu) : 88.11752 89.14212 89.22439 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 84006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33901 grid for indexing accessible points = 1.400000 m= 27067 mr = 55487 m= 3334 mr = 18286 m= 117 mr = 1635 m= 0 mr = 7 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 39109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 26173 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) : 0.5719243 object centre at (A) : 79.41600 41.32450 69.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0237261E-03 5.6899106E-03 midg,1,midg; midg,igrid,midg -1.5776191E-02 2.5125997E-02 1,midg,midg; igrid,midg,midg 7.1849907E-03 -6.5232823E-03 gauss-seidel spectral radius is 0.9984319 estimated iterations to convergence 200 setup time was (sec) 1.220000 now iterating at: 18:27:40 rms-change max change #iterations 4.084905 186.0471 at 10iterations 1.803098 56.35407 at 20iterations 0.7985878 26.73983 at 30iterations 0.3547464 12.22070 at 40iterations 0.1576083 4.904999 at 50iterations 6.9830120E-02 2.109484 at 60iterations 3.1009663E-02 0.9680405 at 70iterations 1.3839334E-02 0.4450340 at 80iterations 6.1721313E-03 0.2037888 at 90iterations 2.7538612E-03 8.5201263E-02 at 100iterations 1.2482177E-03 4.2434692E-02 at 110iterations 5.7770673E-04 1.7051697E-02 at 120iterations finished qdiffx linear iterations at : 18:27:52 total time elapsed so far: 13.01000 # loops : 120 mean,max change (kT/e) : 5.7770673E-04 1.7051697E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 18:27:52 13.230u 0.460s 0:13.97 97.9% 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 Sat Oct 8 2011 at 18:27:52 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3526 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.573659 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): 50.07200 108.7600 ymin,ymax (A): 10.30100 72.34800 zmin,zma (A): 38.43500 100.6810 x,y,z range (A): 58.68800 62.04700 62.24600 scale (grids/A): 2.573659 object centre (A): 79.41600 41.32450 69.55800 number of atom coordinates read : 3526 total number of charged atoms : 3382 net assigned charge : 5.000020 assigned positive charge : 529.5370 centred at (gu) : 86.65401 89.21695 88.95050 assigned negative charge : -524.5386 centred at (gu) : 87.17600 88.71300 88.83660 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 194986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33901 grid for indexing accessible points = 1.400000 m= 90832 mr = 136356 m= 28294 mr = 70619 m= 5406 mr = 21037 m= 477 mr = 3527 m= 18 mr = 173 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.370000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.220000 number of dielectric boundary points 88303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 27040 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) : 1.715773 object centre at (A) : 79.41600 41.32450 69.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3247404E-02 -4.1103072E-02 midg,1,midg; midg,igrid,midg -0.1947196 0.3429689 1,midg,midg; igrid,midg,midg -1.4662722E-02 1.0751407E-02 gauss-seidel spectral radius is 0.9992315 estimated iterations to convergence 285 setup time was (sec) 2.610000 now iterating at: 18:27:55 rms-change max change #iterations 10.34045 309.5347 at 10iterations 6.083397 140.4101 at 20iterations 3.543128 86.80588 at 30iterations 2.055300 41.87410 at 40iterations 1.185961 26.75889 at 50iterations 0.6814918 13.06218 at 60iterations 0.3920062 7.508778 at 70iterations 0.2242337 4.259636 at 80iterations 0.1284390 3.275661 at 90iterations 7.3251188E-02 1.580452 at 100iterations 4.1840695E-02 0.7623711 at 110iterations 2.3964830E-02 0.4701233 at 120iterations 1.3629604E-02 0.2889071 at 130iterations 7.7733765E-03 0.1498184 at 140iterations 4.4386163E-03 8.2174301E-02 at 150iterations 2.5299531E-03 5.3009033E-02 at 160iterations 1.4494120E-03 3.3962250E-02 at 170iterations 8.3312072E-04 1.5863419E-02 at 180iterations finished qdiffx linear iterations at : 18:28:15 total time elapsed so far: 22.28000 # loops : 180 mean,max change (kT/e) : 8.3312072E-04 1.5863419E-02 energy calculations done at 22.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.48000 DelPhi exited at 18:28:16 22.486u 0.508s 0:23.25 98.8% 0+0k 0+0io 0pf+0w