Mon Oct 10 00:27:48 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 Mon Oct 10 2011 at 00:27:49 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: HIR 130 has a net charge of 0.5140 !!! WARNING: HIR 167 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4929314 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 0.4929314 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.45799 assigned positive charge : 844.7102 centred at (gu) : 90.16430 89.08545 90.88841 assigned negative charge : -863.1758 centred at (gu) : 89.98276 89.02222 91.01563 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8722 nv = 96 ne = 84 npr = 114074 no. pairs analyzed = 114074 no. exposed pairs = 7143 no. arc points = 48495 no. surface atoms = 2397 nbur = 3234 mkacc time = 0.2600000 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 = 1.736000 m= 310 mr = 4552 m= 0 mr = 12 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4677 ## 735 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0695143E-11 -3.8039175E-10 midg,1,midg; midg,igrid,midg -2.6185121E-10 -1.9084947E-11 1,midg,midg; igrid,midg,midg -3.6284908E-10 1.4715133E-10 gauss-seidel spectral radius is 0.9790231 estimated iterations to convergence 57 setup time was (sec) 0.7700000 now iterating at: 00:27:49 rms-change max change #iterations 6.3079752E-02 9.862442 at 10iterations 3.9208764E-03 0.5837703 at 20iterations 7.2375970E-04 0.1041737 at 30iterations 2.5616461E-04 3.4874439E-02 at 40iterations 1.0598907E-04 1.7394543E-02 at 50iterations finished qdiffx linear iterations at : 00:27:52 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.0598907E-04 1.7394543E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 00:27:53 3.636u 0.140s 0:04.05 93.0% 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 Mon Oct 10 2011 at 00:27:53 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: HIR 130 has a net charge of 0.5140 !!! WARNING: HIR 167 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.478794 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 1.478794 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.45799 assigned positive charge : 844.7102 centred at (gu) : 90.49090 87.25468 92.66393 assigned negative charge : -863.1758 centred at (gu) : 89.94797 87.06662 93.04688 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28236 mr = 69357 m= 2197 mr = 18338 m= 38 mr = 774 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.7400000 number of dielectric boundary points 41880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 634 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 40679 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) : 0.4929314 object centre at (A) : 18.89050 4.971501 49.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5616180E-03 -2.6807856E-02 midg,1,midg; midg,igrid,midg -1.7427335E-02 5.7463748E-03 1,midg,midg; igrid,midg,midg -3.1159831E-02 8.5376250E-03 gauss-seidel spectral radius is 0.9980313 estimated iterations to convergence 179 setup time was (sec) 1.020000 now iterating at: 00:27:54 rms-change max change #iterations 3.857642 149.1581 at 10iterations 1.551638 53.79182 at 20iterations 0.6231986 21.03957 at 30iterations 0.2507086 7.716332 at 40iterations 0.1010242 3.229316 at 50iterations 4.0728945E-02 1.338196 at 60iterations 1.6453307E-02 0.5207214 at 70iterations 6.6999095E-03 0.2392998 at 80iterations 2.7611351E-03 8.7213516E-02 at 90iterations 1.1728581E-03 4.0007591E-02 at 100iterations 5.3958804E-04 1.7395020E-02 at 110iterations 2.8737946E-04 9.6397400E-03 at 120iterations finished qdiffx linear iterations at : 00:28:01 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.8737946E-04 9.6397400E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 00:28:01 7.929u 0.182s 0:08.37 96.7% 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 Mon Oct 10 2011 at 00:28:01 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 !!! WARNING: HIR 129 has a net charge of 0.5140 !!! WARNING: HIR 130 has a net charge of 0.5140 !!! WARNING: HIR 167 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.218191 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): -17.22000 55.00100 ymin,ymax (A): -29.24800 39.19100 zmin,zma (A): 17.00200 81.10400 x,y,z range (A): 72.22100 68.43900 64.10200 scale (grids/A): 2.218191 object centre (A): 18.89050 4.971501 49.05300 number of atom coordinates read : 5631 total number of charged atoms : 5477 net assigned charge : -18.45799 assigned positive charge : 844.7102 centred at (gu) : 90.73609 85.88155 93.99518 assigned negative charge : -863.1758 centred at (gu) : 89.92183 85.59973 94.57034 start vw surface at 0.2500000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 233288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102618 mr = 170960 m= 24494 mr = 79334 m= 2851 mr = 16928 m= 109 mr = 1584 m= 0 mr = 13 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 1.840000 number of dielectric boundary points 94541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 43651 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) : 1.478794 object centre at (A) : 18.89050 4.971501 49.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1858842E-02 -0.4874077 midg,1,midg; midg,igrid,midg -0.3177679 8.3534740E-02 1,midg,midg; igrid,midg,midg -0.5459706 4.8216041E-02 gauss-seidel spectral radius is 0.9991570 estimated iterations to convergence 272 setup time was (sec) 2.170000 now iterating at: 00:28:03 rms-change max change #iterations 10.85781 300.4680 at 10iterations 6.244033 146.6285 at 20iterations 3.567946 84.35997 at 30iterations 2.018929 47.95323 at 40iterations 1.140063 30.09847 at 50iterations 0.6405932 12.88573 at 60iterations 0.3592635 7.267282 at 70iterations 0.2006934 4.085770 at 80iterations 0.1118682 2.127303 at 90iterations 6.2246639E-02 1.151538 at 100iterations 3.4751661E-02 0.6647320 at 110iterations 1.9332470E-02 0.3341980 at 120iterations 1.0745296E-02 0.1956635 at 130iterations 5.9720520E-03 0.1026859 at 140iterations 3.3290260E-03 6.0813904E-02 at 150iterations 1.8571209E-03 3.1926155E-02 at 160iterations 1.0467980E-03 2.1133423E-02 at 170iterations 5.9744285E-04 1.0253906E-02 at 180iterations finished qdiffx linear iterations at : 00:28:14 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 5.9744285E-04 1.0253906E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 00:28:14 12.702u 0.189s 0:13.15 97.9% 0+0k 0+0io 0pf+0w