Sun Oct 9 16:15:11 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 16:15:11 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 = 3104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6200038 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): -21.17800 35.14800 ymin,ymax (A): 54.38600 106.8930 zmin,zma (A): -1.601000 55.81800 x,y,z range (A): 56.32600 52.50700 57.41900 scale (grids/A): 0.6200038 object centre (A): 6.985000 80.63950 27.10850 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -4.499989 assigned positive charge : 461.6789 centred at (gu) : 90.91486 90.34391 89.95535 assigned negative charge : -466.1802 centred at (gu) : 90.96812 90.22137 90.08183 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7896 nv = 96 ne = 84 npr = 63576 no. pairs analyzed = 63576 no. exposed pairs = 4039 no. arc points = 28208 no. surface atoms = 1357 nbur = 1747 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 4140 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2400000 number of dielectric boundary points 4133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2839 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4139702E-09 -1.3711055E-08 midg,1,midg; midg,igrid,midg -1.2532876E-08 6.5429813E-09 1,midg,midg; igrid,midg,midg 4.7380566E-10 -9.6447055E-09 gauss-seidel spectral radius is 0.9865755 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 16:15:11 rms-change max change #iterations 0.1367335 18.62557 at 10iterations 1.2844134E-02 1.846642 at 20iterations 1.2288975E-03 0.1741514 at 30iterations 1.4154136E-04 1.7791748E-02 at 40iterations 3.0248206E-05 3.4434795E-03 at 50iterations finished qdiffx linear iterations at : 16:15:14 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.0248206E-05 3.4434795E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 16:15:15 3.471u 0.172s 0:03.99 91.2% 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 16:15:15 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 = 3104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.860012 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): -21.17800 35.14800 ymin,ymax (A): 54.38600 106.8930 zmin,zma (A): -1.601000 55.81800 x,y,z range (A): 56.32600 52.50700 57.41900 scale (grids/A): 1.860012 object centre (A): 6.985000 80.63950 27.10850 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -4.499989 assigned positive charge : 461.6789 centred at (gu) : 92.74378 91.03127 89.86499 assigned negative charge : -466.1802 centred at (gu) : 92.90411 90.66389 90.24510 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 85391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28208 grid for indexing accessible points = 1.400000 m= 29235 mr = 58010 m= 4397 mr = 20539 m= 197 mr = 2610 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1616 time to turn everything in is 0.4400000 number of dielectric boundary points 37995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 23238 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) : 0.6200038 object centre at (A) : 6.985000 80.63950 27.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9213594E-02 -2.1728266E-02 midg,1,midg; midg,igrid,midg -2.0150913E-02 -1.0009390E-02 1,midg,midg; igrid,midg,midg -9.3416385E-03 -4.9565259E-02 gauss-seidel spectral radius is 0.9986287 estimated iterations to convergence 214 setup time was (sec) 0.6600000 now iterating at: 16:15:16 rms-change max change #iterations 4.476907 187.9939 at 10iterations 2.078367 67.30861 at 20iterations 0.9711868 29.62274 at 30iterations 0.4532192 14.33549 at 40iterations 0.2123578 6.253187 at 50iterations 9.8925412E-02 2.911033 at 60iterations 4.6051856E-02 1.302450 at 70iterations 2.1579748E-02 0.7060590 at 80iterations 1.0096955E-02 0.3290138 at 90iterations 4.7330610E-03 0.1399565 at 100iterations 2.2172434E-03 6.6247940E-02 at 110iterations 1.0393430E-03 3.6899567E-02 at 120iterations finished qdiffx linear iterations at : 16:15:23 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.0393430E-03 3.6899567E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 16:15:23 8.007u 0.189s 0:08.53 95.8% 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 16:15:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.790017 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): -21.17800 35.14800 ymin,ymax (A): 54.38600 106.8930 zmin,zma (A): -1.601000 55.81800 x,y,z range (A): 56.32600 52.50700 57.41900 scale (grids/A): 2.790017 object centre (A): 6.985000 80.63950 27.10850 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -4.499989 assigned positive charge : 461.6789 centred at (gu) : 94.11520 91.54654 89.79720 assigned negative charge : -466.1802 centred at (gu) : 94.35604 90.99586 90.36761 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 197939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28208 grid for indexing accessible points = 1.400000 m= 95073 mr = 141578 m= 33543 mr = 75559 m= 7718 mr = 26095 m= 934 mr = 5672 m= 42 mr = 578 m= 0 mr = 23 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 5295 time to turn everything in is 1.100000 number of dielectric boundary points 85744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 23695 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) : 1.860012 object centre at (A) : 6.985000 80.63950 27.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7743976 -0.2437638 midg,1,midg; midg,igrid,midg -0.2656196 -0.3041507 1,midg,midg; igrid,midg,midg -0.1269252 -0.6102845 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.340000 now iterating at: 16:15:25 rms-change max change #iterations 10.77620 277.9230 at 10iterations 6.419484 155.4898 at 20iterations 3.803453 77.46902 at 30iterations 2.234688 46.94242 at 40iterations 1.309273 27.05691 at 50iterations 0.7658807 14.41453 at 60iterations 0.4475838 8.896719 at 70iterations 0.2611991 4.406511 at 80iterations 0.1520661 3.253932 at 90iterations 8.8398345E-02 1.553248 at 100iterations 5.1348500E-02 0.9614563 at 110iterations 2.9807087E-02 0.5768356 at 120iterations 1.7316887E-02 0.3201141 at 130iterations 1.0009594E-02 0.1799736 at 140iterations 5.8264090E-03 0.1126251 at 150iterations 3.3839920E-03 5.3833008E-02 at 160iterations 1.9591753E-03 3.4168243E-02 at 170iterations 1.1348693E-03 2.0176888E-02 at 180iterations finished qdiffx linear iterations at : 16:15:36 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.1348693E-03 2.0176888E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 16:15:37 13.038u 0.207s 0:13.52 97.8% 0+0k 0+0io 0pf+0w