Sun Oct 9 08:15:23 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 Sun Oct 9 2011 at 08:15:23 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4355167 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 0.4355167 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 528.1434 centred at (gu) : 91.59185 83.01503 89.87236 assigned negative charge : -516.6451 centred at (gu) : 91.63458 83.11636 89.80956 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 4325 nv = 96 ne = 84 npr = 72798 no. pairs analyzed = 72798 no. exposed pairs = 4776 no. arc points = 35188 no. surface atoms = 1595 nbur = 2073 mkacc time = 0.1600000 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 = 1.932000 m= 109 mr = 1952 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2786 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 5671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7471942E-13 5.0035683E-12 midg,1,midg; midg,igrid,midg 6.1486594E-11 -1.4721026E-13 1,midg,midg; igrid,midg,midg 2.7435363E-12 1.5326580E-12 gauss-seidel spectral radius is 0.9730566 estimated iterations to convergence 51 setup time was (sec) 0.6100000 now iterating at: 08:15:24 rms-change max change #iterations 2.4169099E-02 5.292299 at 10iterations 1.0757273E-03 0.2321911 at 20iterations 1.7534518E-04 3.3202052E-02 at 30iterations 3.9222839E-05 7.6302290E-03 at 40iterations 8.9483465E-06 1.7462969E-03 at 50iterations finished qdiffx linear iterations at : 08:15:27 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.9483465E-06 1.7462969E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 08:15:27 3.591u 0.261s 0:04.16 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 08:15:27 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.306550 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 1.306550 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 528.1434 centred at (gu) : 94.77462 69.04445 89.61618 assigned negative charge : -516.6451 centred at (gu) : 94.90337 69.34866 89.42801 start vw surface at 0.1700000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 49805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 11068 mr = 31695 m= 579 mr = 6482 m= 10 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1355 time to turn everything in is 0.4200000 number of dielectric boundary points 23154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 593 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 23768 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) : 0.4355167 object centre at (A) : -4.462501 18.59800 16.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4261600E-03 2.3798945E-03 midg,1,midg; midg,igrid,midg 1.5124377E-02 -2.8608361E-04 1,midg,midg; igrid,midg,midg 7.9537596E-04 6.6721106E-05 gauss-seidel spectral radius is 0.9971245 estimated iterations to convergence 149 setup time was (sec) 0.7200000 now iterating at: 08:15:28 rms-change max change #iterations 2.101458 138.5900 at 10iterations 0.7032281 45.41782 at 20iterations 0.2351424 12.02170 at 30iterations 7.8107297E-02 3.751221 at 40iterations 2.6126416E-02 1.132359 at 50iterations 8.6973114E-03 0.4598579 at 60iterations 2.9228402E-03 0.1558361 at 70iterations 9.9749444E-04 4.5925140E-02 at 80iterations 3.4899425E-04 1.6677856E-02 at 90iterations 1.3147239E-04 5.6793690E-03 at 100iterations 5.6925597E-05 2.4662018E-03 at 110iterations 2.8052120E-05 1.2207031E-03 at 120iterations finished qdiffx linear iterations at : 08:15:36 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 2.8052120E-05 1.2207031E-03 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.690000 DelPhi exited at 08:15:37 8.694u 0.285s 0:09.34 96.0% 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 Sun Oct 9 2011 at 08:15:37 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3668 !!! WARNING: NAP 1027 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.959825 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): -30.86400 21.93900 ymin,ymax (A): -22.27300 59.46900 zmin,zma (A): -17.19200 49.59600 x,y,z range (A): 52.80300 81.74200 66.78800 scale (grids/A): 1.959825 object centre (A): -4.462501 18.59800 16.20200 number of atom coordinates read : 3668 total number of charged atoms : 3384 net assigned charge : 11.50005 assigned positive charge : 528.1434 centred at (gu) : 97.16174 58.56655 89.42410 assigned negative charge : -516.6451 centred at (gu) : 97.35503 59.02286 89.14205 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 116476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35188 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 43115 mr = 78891 m= 7604 mr = 31574 m= 589 mr = 4854 m= 7 mr = 230 m= 0 mr = 2 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 4651 time to turn everything in is 0.8900000 number of dielectric boundary points 52240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26734 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) : 1.306550 object centre at (A) : -4.462501 18.59800 16.20200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0496379E-02 4.7256663E-02 midg,1,midg; midg,igrid,midg 0.4326537 1.2716769E-03 1,midg,midg; igrid,midg,midg 1.5403310E-02 -1.1918559E-02 gauss-seidel spectral radius is 0.9987326 estimated iterations to convergence 222 setup time was (sec) 1.210000 now iterating at: 08:15:38 rms-change max change #iterations 6.330984 276.2412 at 10iterations 3.188221 116.0368 at 20iterations 1.587359 54.03303 at 30iterations 0.7849799 27.96478 at 40iterations 0.3855046 13.08340 at 50iterations 0.1892055 6.043286 at 60iterations 9.2544608E-02 2.693195 at 70iterations 4.5198500E-02 1.329565 at 80iterations 2.1978024E-02 0.7377539 at 90iterations 1.0671920E-02 0.3526726 at 100iterations 5.1882276E-03 0.1592159 at 110iterations 2.5241440E-03 6.8963528E-02 at 120iterations 1.2249864E-03 3.7198067E-02 at 130iterations 5.9477420E-04 1.8260956E-02 at 140iterations 2.8887371E-04 8.4915161E-03 at 150iterations 1.4049902E-04 4.0893555E-03 at 160iterations 6.8425514E-05 1.8367767E-03 at 170iterations 3.3507833E-05 9.4223022E-04 at 180iterations finished qdiffx linear iterations at : 08:15:49 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 3.3507833E-05 9.4223022E-04 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 08:15:49 11.668u 0.305s 0:12.49 95.7% 0+0k 0+0io 0pf+0w