Sun Oct 9 08:19:11 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 Sun Oct 9 2011 at 08:19:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4804772 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 0.4804772 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.500043 assigned positive charge : 908.4960 centred at (gu) : 90.43034 90.68380 90.38113 assigned negative charge : -906.0037 centred at (gu) : 90.39719 90.77230 90.29285 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8433 nv = 96 ne = 84 npr = 122308 no. pairs analyzed = 122308 no. exposed pairs = 7617 no. arc points = 52087 no. surface atoms = 2555 nbur = 3473 mkacc time = 0.2600000 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 = 1.764000 m= 266 mr = 4208 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5400000 number of dielectric boundary points 4488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4871 ## 835 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9393580E-11 9.0999611E-11 midg,1,midg; midg,igrid,midg 6.7601889E-11 -8.0704991E-11 1,midg,midg; igrid,midg,midg -1.6969488E-11 4.0994961E-11 gauss-seidel spectral radius is 0.9779443 estimated iterations to convergence 56 setup time was (sec) 0.7500000 now iterating at: 08:19:12 rms-change max change #iterations 5.6302220E-02 9.386618 at 10iterations 3.0159615E-03 0.5229111 at 20iterations 3.7881822E-04 8.5899353E-02 at 30iterations 1.0178368E-04 2.1886826E-02 at 40iterations 3.0425148E-05 6.0882568E-03 at 50iterations finished qdiffx linear iterations at : 08:19:15 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.0425148E-05 6.0882568E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:19:15 3.341u 0.151s 0:03.77 92.5% 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 Sun Oct 9 2011 at 08:19:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.441432 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 1.441432 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.500043 assigned positive charge : 908.4960 centred at (gu) : 91.28943 92.04946 91.14121 assigned negative charge : -906.0037 centred at (gu) : 91.19126 92.31637 90.87814 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 95878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52087 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25465 mr = 64388 m= 1791 mr = 16115 m= 22 mr = 578 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 0.6700000 number of dielectric boundary points 42075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 858 ## 21 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 42999 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) : 0.4804772 object centre at (A) : 109.9680 -79.76300 -50.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2634363E-03 9.2910919E-03 midg,1,midg; midg,igrid,midg 5.2240430E-03 -1.2297059E-03 1,midg,midg; igrid,midg,midg -7.5760931E-03 8.7211211E-04 gauss-seidel spectral radius is 0.9979454 estimated iterations to convergence 175 setup time was (sec) 0.9500000 now iterating at: 08:19:16 rms-change max change #iterations 3.736784 145.1354 at 10iterations 1.469176 53.64164 at 20iterations 0.5813178 21.14667 at 30iterations 0.2292408 7.750925 at 40iterations 9.0624504E-02 3.002227 at 50iterations 3.5856124E-02 1.098595 at 60iterations 1.4220627E-02 0.4607549 at 70iterations 5.6416802E-03 0.1780930 at 80iterations 2.2614521E-03 7.2900772E-02 at 90iterations 9.2759385E-04 3.0731201E-02 at 100iterations 3.9509917E-04 1.4545441E-02 at 110iterations 1.8206981E-04 6.7214966E-03 at 120iterations finished qdiffx linear iterations at : 08:19:22 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 1.8206981E-04 6.7214966E-03 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 08:19:23 7.228u 0.180s 0:07.92 93.4% 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 Sun Oct 9 2011 at 08:19:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6028 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.162148 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): 76.87100 143.0650 ymin,ymax (A): -111.6130 -47.91300 zmin,zma (A): -87.35800 -13.26500 x,y,z range (A): 66.19398 63.70000 74.09300 scale (grids/A): 2.162148 object centre (A): 109.9680 -79.76300 -50.31150 number of atom coordinates read : 6028 total number of charged atoms : 5861 net assigned charge : 2.500043 assigned positive charge : 908.4960 centred at (gu) : 91.93376 93.07371 91.71139 assigned negative charge : -906.0037 centred at (gu) : 91.78696 93.47458 91.31723 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 224056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52087 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 94055 mr = 159452 m= 21007 mr = 71542 m= 2207 mr = 14256 m= 58 mr = 1103 m= 0 mr = 8 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 2971 time to turn everything in is 1.540000 number of dielectric boundary points 95022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 46641 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) : 1.441432 object centre at (A) : 109.9680 -79.76300 -50.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2529472 1.7705599E-02 midg,1,midg; midg,igrid,midg 9.1887355E-02 -9.4660772E-03 1,midg,midg; igrid,midg,midg -0.2006725 1.0828275E-02 gauss-seidel spectral radius is 0.9991402 estimated iterations to convergence 269 setup time was (sec) 1.840000 now iterating at: 08:19:25 rms-change max change #iterations 10.63079 348.4063 at 10iterations 6.061987 153.9287 at 20iterations 3.439087 83.18335 at 30iterations 1.939471 47.30579 at 40iterations 1.092432 30.32813 at 50iterations 0.6110079 11.74150 at 60iterations 0.3420954 7.054911 at 70iterations 0.1908793 3.726193 at 80iterations 0.1062367 2.192146 at 90iterations 5.9105121E-02 1.105633 at 100iterations 3.2863989E-02 0.6218834 at 110iterations 1.8247269E-02 0.3659592 at 120iterations 1.0127816E-02 0.1982570 at 130iterations 5.6211953E-03 0.1076822 at 140iterations 3.1301565E-03 5.9942245E-02 at 150iterations 1.7416240E-03 3.2019615E-02 at 160iterations 9.7281195E-04 1.8379211E-02 at 170iterations 5.4840842E-04 1.0287285E-02 at 180iterations finished qdiffx linear iterations at : 08:19:35 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 5.4840842E-04 1.0287285E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 08:19:35 11.801u 0.181s 0:12.25 97.7% 0+0k 0+0io 0pf+0w