Sun Oct 9 08:03:23 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+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 08:03:23 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6948375 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 0.6948375 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.03302 91.04145 90.22890 assigned negative charge : -342.2557 centred at (gu) : 90.06461 91.12355 90.33719 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7504 nv = 96 ne = 84 npr = 44249 no. pairs analyzed = 44249 no. exposed pairs = 2898 no. arc points = 20809 no. surface atoms = 966 nbur = 1266 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4093 m= 6 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 3855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1985 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8299 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1289981E-08 -6.8874961E-08 midg,1,midg; midg,igrid,midg 9.4325170E-09 -6.7628250E-08 1,midg,midg; igrid,midg,midg -8.3746512E-09 -3.4355832E-08 gauss-seidel spectral radius is 0.9892328 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 08:03:24 rms-change max change #iterations 0.1976167 31.81837 at 10iterations 2.3174062E-02 3.494572 at 20iterations 2.7548578E-03 0.3973770 at 30iterations 3.2557963E-04 4.4854164E-02 at 40iterations 3.8742699E-05 4.8680305E-03 at 50iterations finished qdiffx linear iterations at : 08:03:27 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.8742699E-05 4.8680305E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:03:27 3.553u 0.205s 0:04.05 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 08:03:27 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.084512 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 2.084512 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.09864 93.12398 90.68619 assigned negative charge : -342.2557 centred at (gu) : 90.19357 93.37060 91.01162 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20809 grid for indexing accessible points = 1.400000 m= 32003 mr = 54246 m= 6631 mr = 24081 m= 663 mr = 4471 m= 25 mr = 324 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 485 time to turn everything in is 0.4000000 number of dielectric boundary points 35305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 16582 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) : 0.6948375 object centre at (A) : 27.34350 0.8055000 5.348500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9055214E-03 -4.1955791E-02 midg,1,midg; midg,igrid,midg 2.3160957E-02 -3.4595316E-03 1,midg,midg; igrid,midg,midg -5.3775602E-04 -3.4048107E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 0.6200000 now iterating at: 08:03:28 rms-change max change #iterations 4.771646 206.6096 at 10iterations 2.351610 82.37427 at 20iterations 1.168076 39.46737 at 30iterations 0.5729789 17.67572 at 40iterations 0.2838011 8.892076 at 50iterations 0.1400393 4.473573 at 60iterations 6.9389574E-02 2.231226 at 70iterations 3.4133647E-02 1.001211 at 80iterations 1.6913967E-02 0.5196223 at 90iterations 8.3674304E-03 0.2501183 at 100iterations 4.1363100E-03 0.1226044 at 110iterations 2.0427811E-03 5.6058884E-02 at 120iterations finished qdiffx linear iterations at : 08:03:35 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 2.0427811E-03 5.6058884E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 08:03:36 8.119u 0.233s 0:08.60 96.9% 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 Sun Oct 9 2011 at 08:03:36 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.126769 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): 4.610000 50.07700 ymin,ymax (A): -24.81200 26.42300 zmin,zma (A): -19.59200 30.28900 x,y,z range (A): 45.46700 51.23500 49.88100 scale (grids/A): 3.126769 object centre (A): 27.34350 0.8055000 5.348500 number of atom coordinates read : 2232 total number of charged atoms : 2090 net assigned charge : -3.499991 assigned positive charge : 338.7554 centred at (gu) : 90.14809 94.68583 91.02927 assigned negative charge : -342.2557 centred at (gu) : 90.29032 95.05589 91.51743 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 181980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20809 grid for indexing accessible points = 1.400000 m= 98043 mr = 130631 m= 41709 mr = 80823 m= 12578 mr = 34356 m= 2631 mr = 9760 m= 310 mr = 1891 m= 14 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 1584 time to turn everything in is 1.230000 number of dielectric boundary points 79643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 16720 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) : 2.084512 object centre at (A) : 27.34350 0.8055000 5.348500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9733965E-02 -0.2825932 midg,1,midg; midg,igrid,midg 0.8013201 6.5276496E-02 1,midg,midg; igrid,midg,midg -2.5030343E-02 -0.3055435 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.480000 now iterating at: 08:03:38 rms-change max change #iterations 10.74518 500.7236 at 10iterations 6.315475 127.8175 at 20iterations 3.702941 79.11740 at 30iterations 2.173179 39.92924 at 40iterations 1.273040 23.11685 at 50iterations 0.7452930 13.12526 at 60iterations 0.4364679 8.382012 at 70iterations 0.2551205 4.603038 at 80iterations 0.1487987 2.602396 at 90iterations 8.6906202E-02 1.477844 at 100iterations 5.0869625E-02 0.8735771 at 110iterations 2.9622920E-02 0.4803543 at 120iterations 1.7274860E-02 0.2798185 at 130iterations 1.0086745E-02 0.1673946 at 140iterations 5.8969161E-03 0.1007404 at 150iterations 3.4396411E-03 5.7159424E-02 at 160iterations 2.0173511E-03 3.7372589E-02 at 170iterations 1.1851819E-03 1.8747330E-02 at 180iterations finished qdiffx linear iterations at : 08:03:50 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.1851819E-03 1.8747330E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 08:03:50 13.499u 0.231s 0:13.99 98.0% 0+0k 0+0io 0pf+0w