Sun Oct 9 10:22:28 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 10:22:28 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 = 2200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6684819 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): -1.698000 48.24700 ymin,ymax (A): -26.82600 26.42900 zmin,zma (A): -4.094000 47.38800 x,y,z range (A): 49.94500 53.25500 51.48200 scale (grids/A): 0.6684819 object centre (A): 23.27450 -0.1985006 21.64700 number of atom coordinates read : 2200 total number of charged atoms : 2063 net assigned charge : 0.5000171 assigned positive charge : 318.0886 centred at (gu) : 90.65474 92.46351 90.89874 assigned negative charge : -317.5893 centred at (gu) : 90.67474 92.35358 90.81660 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6778 nv = 96 ne = 84 npr = 44232 no. pairs analyzed = 44232 no. exposed pairs = 2975 no. arc points = 21362 no. surface atoms = 990 nbur = 1210 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3485 m= 0 mr = 69 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2025 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2952935E-08 2.0628624E-08 midg,1,midg; midg,igrid,midg -1.2762944E-08 3.7975941E-08 1,midg,midg; igrid,midg,midg 4.2285482E-09 -3.6122174E-09 gauss-seidel spectral radius is 0.9883741 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 10:22:28 rms-change max change #iterations 0.1563742 21.23069 at 10iterations 1.7051404E-02 2.554354 at 20iterations 1.8520119E-03 0.2955704 at 30iterations 2.0229946E-04 2.7423859E-02 at 40iterations 2.1771641E-05 3.1936169E-03 at 50iterations finished qdiffx linear iterations at : 10:22:31 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.1771641E-05 3.1936169E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 10:22:32 3.397u 0.175s 0:03.93 90.5% 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 10:22:32 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 = 2200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.005446 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): -1.698000 48.24700 ymin,ymax (A): -26.82600 26.42900 zmin,zma (A): -4.094000 47.38800 x,y,z range (A): 49.94500 53.25500 51.48200 scale (grids/A): 2.005446 object centre (A): 23.27450 -0.1985006 21.64700 number of atom coordinates read : 2200 total number of charged atoms : 2063 net assigned charge : 0.5000171 assigned positive charge : 318.0886 centred at (gu) : 91.96394 97.38985 92.69577 assigned negative charge : -317.5893 centred at (gu) : 92.02448 97.06094 92.45001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21362 grid for indexing accessible points = 1.400000 m= 26079 mr = 47806 m= 4901 mr = 18764 m= 493 mr = 3277 m= 11 mr = 255 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 924 time to turn everything in is 0.3700000 number of dielectric boundary points 33538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16345 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) : 0.6684819 object centre at (A) : 23.27450 -0.1985006 21.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1801496E-02 5.0720155E-02 midg,1,midg; midg,igrid,midg -4.6537630E-03 4.0642414E-02 1,midg,midg; igrid,midg,midg -1.7937634E-02 -2.0640308E-02 gauss-seidel spectral radius is 0.9987329 estimated iterations to convergence 223 setup time was (sec) 0.5900000 now iterating at: 10:22:33 rms-change max change #iterations 4.174935 217.2961 at 10iterations 2.004742 72.93199 at 20iterations 0.9721003 41.29103 at 30iterations 0.4665484 14.59811 at 40iterations 0.2259591 7.850350 at 50iterations 0.1090284 3.734165 at 60iterations 5.2463491E-02 1.836613 at 70iterations 2.5288733E-02 0.8205686 at 80iterations 1.2130329E-02 0.4137369 at 90iterations 5.8393930E-03 0.1828003 at 100iterations 2.8111134E-03 8.7661743E-02 at 110iterations 1.3540250E-03 4.5655370E-02 at 120iterations finished qdiffx linear iterations at : 10:22:40 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.3540250E-03 4.5655370E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 10:22:40 7.923u 0.208s 0:08.44 96.2% 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 Sun Oct 9 2011 at 10:22:40 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 = 2200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.008168 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): -1.698000 48.24700 ymin,ymax (A): -26.82600 26.42900 zmin,zma (A): -4.094000 47.38800 x,y,z range (A): 49.94500 53.25500 51.48200 scale (grids/A): 3.008168 object centre (A): 23.27450 -0.1985006 21.64700 number of atom coordinates read : 2200 total number of charged atoms : 2063 net assigned charge : 0.5000171 assigned positive charge : 318.0886 centred at (gu) : 92.94590 101.0848 94.04365 assigned negative charge : -317.5893 centred at (gu) : 93.03664 100.5914 93.67507 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21362 grid for indexing accessible points = 1.400000 m= 81815 mr = 116176 m= 31792 mr = 65463 m= 9212 mr = 25474 m= 1910 mr = 7185 m= 228 mr = 1494 m= 7 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 3052 time to turn everything in is 0.9400000 number of dielectric boundary points 75673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 16503 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) : 2.005446 object centre at (A) : 23.27450 -0.1985006 21.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2836452 0.5883603 midg,1,midg; midg,igrid,midg -6.4908251E-02 0.3020556 1,midg,midg; igrid,midg,midg -0.2251147 -0.2404041 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 1.170000 now iterating at: 10:22:42 rms-change max change #iterations 9.711722 492.3934 at 10iterations 5.678198 128.8207 at 20iterations 3.328588 71.28391 at 30iterations 1.946057 41.37557 at 40iterations 1.134586 23.38415 at 50iterations 0.6615670 11.54516 at 60iterations 0.3850178 8.036766 at 70iterations 0.2238413 4.302719 at 80iterations 0.1300319 2.485341 at 90iterations 7.5823344E-02 1.502409 at 100iterations 4.3964259E-02 0.9300795 at 110iterations 2.5567411E-02 0.4738607 at 120iterations 1.4865867E-02 0.2615013 at 130iterations 8.6488379E-03 0.1589522 at 140iterations 5.0156224E-03 8.8995934E-02 at 150iterations 2.9204173E-03 5.2975655E-02 at 160iterations 1.6953005E-03 2.8789520E-02 at 170iterations 9.8754559E-04 1.8813133E-02 at 180iterations finished qdiffx linear iterations at : 10:22:54 total time elapsed so far: 13.74000 # loops : 180 mean,max change (kT/e) : 9.8754559E-04 1.8813133E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 10:22:55 13.879u 0.221s 0:14.46 97.4% 0+0k 0+0io 0pf+0w