Mon Oct 10 17:00:44 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 Mon Oct 10 2011 at 17:00:44 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5125989 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 0.5125989 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4545 net assigned charge : 3.800028 assigned positive charge : 719.1074 centred at (gu) : 90.33541 90.37537 88.34920 assigned negative charge : -715.3120 centred at (gu) : 90.22612 90.39176 88.41884 start vw surface at 0.2400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7820 nv = 96 ne = 84 npr = 96046 no. pairs analyzed = 96046 no. exposed pairs = 6063 no. arc points = 41594 no. surface atoms = 2028 nbur = 2721 mkacc time = 0.2000000 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 = 1.652000 m= 279 mr = 4018 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4080 ## 624 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8661915E-10 -9.2337749E-11 midg,1,midg; midg,igrid,midg 9.1173000E-11 8.5422268E-12 1,midg,midg; igrid,midg,midg -2.3620572E-10 3.9152317E-10 gauss-seidel spectral radius is 0.9805328 estimated iterations to convergence 59 setup time was (sec) 0.7000000 now iterating at: 17:00:45 rms-change max change #iterations 6.9625184E-02 11.80716 at 10iterations 4.2452961E-03 0.6124220 at 20iterations 5.9016416E-04 7.7246666E-02 at 30iterations 2.0175122E-04 3.1092167E-02 at 40iterations 7.6416021E-05 1.2297392E-02 at 50iterations finished qdiffx linear iterations at : 17:00:48 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 7.6416021E-05 1.2297392E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 17:00:48 3.277u 0.129s 0:04.08 83.0% 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 Mon Oct 10 2011 at 17:00:48 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.537797 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 1.537797 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4545 net assigned charge : 3.800028 assigned positive charge : 719.1074 centred at (gu) : 91.00480 91.12446 85.04604 assigned negative charge : -715.3120 centred at (gu) : 90.67825 91.17529 85.25633 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 88155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25714 mr = 60122 m= 2224 mr = 16950 m= 41 mr = 931 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.6300000 number of dielectric boundary points 38129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 538 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 34247 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) : 0.5125989 object centre at (A) : 8.987501 2.053000 30.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2885058E-03 -6.9733551E-03 midg,1,midg; midg,igrid,midg 6.5106433E-03 -5.4997439E-03 1,midg,midg; igrid,midg,midg -1.5899331E-03 1.1626119E-02 gauss-seidel spectral radius is 0.9981250 estimated iterations to convergence 184 setup time was (sec) 0.9000000 now iterating at: 17:00:50 rms-change max change #iterations 3.844513 163.6137 at 10iterations 1.577194 53.22852 at 20iterations 0.6475340 20.78116 at 30iterations 0.2663580 9.216656 at 40iterations 0.1100009 3.548332 at 50iterations 4.5261528E-02 1.427426 at 60iterations 1.8626451E-02 0.5752563 at 70iterations 7.7414736E-03 0.2284927 at 80iterations 3.2468452E-03 0.1071453 at 90iterations 1.3944545E-03 4.2770386E-02 at 100iterations 6.3852355E-04 2.2753716E-02 at 110iterations 3.2930871E-04 1.1278152E-02 at 120iterations finished qdiffx linear iterations at : 17:00:56 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 3.2930871E-04 1.1278152E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 17:00:56 7.130u 0.185s 0:07.92 92.2% 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 Mon Oct 10 2011 at 17:00:56 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4749 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: ZN8 822 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.306695 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): -18.46700 36.44200 ymin,ymax (A): -30.27500 34.38100 zmin,zma (A): -4.080000 65.37000 x,y,z range (A): 54.90900 64.65600 69.45000 scale (grids/A): 2.306695 object centre (A): 8.987501 2.053000 30.64500 number of atom coordinates read : 4749 total number of charged atoms : 4545 net assigned charge : 3.800028 assigned positive charge : 719.1074 centred at (gu) : 91.50684 91.68652 82.56881 assigned negative charge : -715.3120 centred at (gu) : 91.01747 91.76265 82.88450 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 205883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91701 mr = 148377 m= 23093 mr = 71139 m= 3202 mr = 16466 m= 187 mr = 1887 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 148 time to turn everything in is 1.490000 number of dielectric boundary points 86139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 36266 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) : 1.537797 object centre at (A) : 8.987501 2.053000 30.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1752944 -0.1672428 midg,1,midg; midg,igrid,midg 0.1072142 -0.1501355 1,midg,midg; igrid,midg,midg -1.9093562E-02 0.1792719 gauss-seidel spectral radius is 0.9991657 estimated iterations to convergence 273 setup time was (sec) 1.780000 now iterating at: 17:00:58 rms-change max change #iterations 10.37454 319.0513 at 10iterations 5.968180 149.8521 at 20iterations 3.407089 90.05634 at 30iterations 1.924222 43.95986 at 40iterations 1.087290 22.85522 at 50iterations 0.6125892 12.11976 at 60iterations 0.3436500 7.357509 at 70iterations 0.1923550 4.025667 at 80iterations 0.1075339 2.190308 at 90iterations 5.9966303E-02 1.126993 at 100iterations 3.3464879E-02 0.7234927 at 110iterations 1.8702246E-02 0.3580818 at 120iterations 1.0411242E-02 0.2034187 at 130iterations 5.8045331E-03 0.1272984 at 140iterations 3.2364365E-03 7.2353363E-02 at 150iterations 1.8134771E-03 3.7355423E-02 at 160iterations 1.0196926E-03 1.8890381E-02 at 170iterations 5.7886913E-04 1.2290955E-02 at 180iterations finished qdiffx linear iterations at : 17:01:08 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 5.7886913E-04 1.2290955E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 17:01:09 11.756u 0.188s 0:12.83 92.9% 0+0k 0+0io 0pf+0w