Sun Oct 9 10:22:55 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 10:22:55 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 = 2200 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 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 : 0.5140161 assigned positive charge : 320.5306 centred at (gu) : 90.70674 92.44470 90.91949 assigned negative charge : -320.0173 centred at (gu) : 90.72501 92.33301 90.83870 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 0.2400000 number of grid points assigned charge 7779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2747519E-08 2.0587159E-08 midg,1,midg; midg,igrid,midg -1.3111807E-08 3.8734473E-08 1,midg,midg; igrid,midg,midg 3.9396895E-09 -3.2463934E-09 gauss-seidel spectral radius is 0.9883741 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 10:22:55 rms-change max change #iterations 0.1586969 22.60890 at 10iterations 1.7304402E-02 2.461988 at 20iterations 1.8823743E-03 0.3017769 at 30iterations 2.0554884E-04 2.7153969E-02 at 40iterations 2.2176466E-05 3.0652285E-03 at 50iterations finished qdiffx linear iterations at : 10:22:58 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.2176466E-05 3.0652285E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 10:22:59 3.323u 0.168s 0:03.90 89.2% 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 10:22:59 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 = 2200 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 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 : 0.5140161 assigned positive charge : 320.5306 centred at (gu) : 92.11993 97.33345 92.75803 assigned negative charge : -320.0173 centred at (gu) : 92.17529 96.99921 92.51629 start vw surface at 7.9999998E-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 = 0.1600000 no. cavity mid-points inaccessible to solvent = 924 time to turn everything in is 0.3600000 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 0.4400000 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 -2.1687532E-02 5.0603304E-02 midg,1,midg; midg,igrid,midg -4.7199372E-03 4.1838273E-02 1,midg,midg; igrid,midg,midg -1.8402923E-02 -2.1621577E-02 gauss-seidel spectral radius is 0.9987329 estimated iterations to convergence 223 setup time was (sec) 0.5800000 now iterating at: 10:23:00 rms-change max change #iterations 4.208966 217.2962 at 10iterations 2.021685 71.78232 at 20iterations 0.9801453 41.23318 at 30iterations 0.4706472 14.64833 at 40iterations 0.2278584 7.966971 at 50iterations 0.1099427 3.703411 at 60iterations 5.2893683E-02 1.822121 at 70iterations 2.5492677E-02 0.8753281 at 80iterations 1.2228932E-02 0.4165367 at 90iterations 5.8877314E-03 0.1847759 at 100iterations 2.8352733E-03 8.8233948E-02 at 110iterations 1.3653028E-03 4.6164989E-02 at 120iterations finished qdiffx linear iterations at : 10:23:07 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.3653028E-03 4.6164989E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 10:23:07 7.823u 0.186s 0:08.47 94.4% 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 10:23:07 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 = 2200 !!! WARNING: HIR 524 has a net charge of 0.5140 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 : 0.5140161 assigned positive charge : 320.5306 centred at (gu) : 93.17986 101.0002 94.13702 assigned negative charge : -320.0173 centred at (gu) : 93.26284 100.4989 93.77448 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 0.9300000 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 -0.2825118 0.5858949 midg,1,midg; midg,igrid,midg -6.6412069E-02 0.3145771 1,midg,midg; igrid,midg,midg -0.2296509 -0.2564068 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 1.170000 now iterating at: 10:23:09 rms-change max change #iterations 9.793543 492.3931 at 10iterations 5.725690 128.8206 at 20iterations 3.355961 71.49409 at 30iterations 1.962123 42.72664 at 40iterations 1.143459 23.53680 at 50iterations 0.6667430 11.71185 at 60iterations 0.3879361 8.004147 at 70iterations 0.2255307 4.374837 at 80iterations 0.1310341 2.509825 at 90iterations 7.6389231E-02 1.532854 at 100iterations 4.4300783E-02 0.9589634 at 110iterations 2.5761349E-02 0.4769049 at 120iterations 1.4977360E-02 0.2669469 at 130iterations 8.7149665E-03 0.1627921 at 140iterations 5.0520860E-03 9.0960264E-02 at 150iterations 2.9415854E-03 5.3409576E-02 at 160iterations 1.7067796E-03 2.8541565E-02 at 170iterations 9.9504564E-04 1.9573212E-02 at 180iterations finished qdiffx linear iterations at : 10:23:20 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 9.9504564E-04 1.9573212E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 10:23:21 12.705u 0.211s 0:13.22 97.6% 0+0k 0+0io 0pf+0w