Tue Oct 11 03:14:51 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 Tue Oct 11 2011 at 03:14:51 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3166 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5342938 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 0.5342938 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3023 net assigned charge : -6.093974 assigned positive charge : 475.1739 centred at (gu) : 88.79947 91.47923 93.02156 assigned negative charge : -481.2689 centred at (gu) : 88.84442 91.46826 93.04819 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5694 nv = 96 ne = 84 npr = 65591 no. pairs analyzed = 65591 no. exposed pairs = 3907 no. arc points = 27401 no. surface atoms = 1315 nbur = 1851 mkacc time = 0.1400000 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 = 1.596000 m= 215 mr = 2969 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6687269E-11 -7.6214207E-10 midg,1,midg; midg,igrid,midg -1.9703231E-10 -2.6356070E-10 1,midg,midg; igrid,midg,midg -3.7956718E-11 -3.2485684E-10 gauss-seidel spectral radius is 0.9819573 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 03:14:52 rms-change max change #iterations 7.0355915E-02 15.97610 at 10iterations 4.4778003E-03 0.7117271 at 20iterations 3.3227535E-04 5.7655334E-02 at 30iterations 4.0930954E-05 7.6545477E-03 at 40iterations 7.7281466E-06 1.6076565E-03 at 50iterations finished qdiffx linear iterations at : 03:14:54 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 7.7281466E-06 1.6076565E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 03:14:55 3.334u 0.203s 0:03.86 91.4% 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 Tue Oct 11 2011 at 03:14:55 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3166 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.602881 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 1.602881 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3023 net assigned charge : -6.093974 assigned positive charge : 475.1739 centred at (gu) : 86.39784 94.43714 99.06382 assigned negative charge : -481.2689 centred at (gu) : 86.53289 94.40407 99.14440 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19012 mr = 42753 m= 1817 mr = 13174 m= 39 mr = 869 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 275 time to turn everything in is 0.4700000 number of dielectric boundary points 27350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 23031 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) : 0.5342938 object centre at (A) : 14.20650 97.18900 139.4030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3586985E-02 -1.2810841E-02 midg,1,midg; midg,igrid,midg -3.3467792E-03 3.9477586E-03 1,midg,midg; igrid,midg,midg -3.0907670E-03 -5.9019611E-03 gauss-seidel spectral radius is 0.9981190 estimated iterations to convergence 183 setup time was (sec) 0.7600000 now iterating at: 03:14:56 rms-change max change #iterations 3.318482 150.4168 at 10iterations 1.357657 51.67926 at 20iterations 0.5587487 21.63689 at 30iterations 0.2294749 7.963013 at 40iterations 9.4752260E-02 3.422386 at 50iterations 3.8858175E-02 1.328601 at 60iterations 1.5960462E-02 0.6219928 at 70iterations 6.5541160E-03 0.2567720 at 80iterations 2.6994837E-03 9.1163635E-02 at 90iterations 1.1178561E-03 4.1305289E-02 at 100iterations 4.6488177E-04 1.8666744E-02 at 110iterations 1.9592347E-04 7.2689056E-03 at 120iterations finished qdiffx linear iterations at : 03:15:02 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.9592347E-04 7.2689056E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 03:15:03 7.364u 0.226s 0:07.92 95.7% 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 Tue Oct 11 2011 at 03:15:03 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3166 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.404322 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 2.404322 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3023 net assigned charge : -6.093974 assigned positive charge : 475.1739 centred at (gu) : 84.59665 96.65565 103.5954 assigned negative charge : -481.2689 centred at (gu) : 84.79930 96.60606 103.7164 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 147061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66711 mr = 104729 m= 18276 mr = 52764 m= 2784 mr = 13837 m= 165 mr = 1791 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 1.080000 number of dielectric boundary points 61825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 24139 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) : 1.602881 object centre at (A) : 14.20650 97.18900 139.4030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4224990 -0.3344192 midg,1,midg; midg,igrid,midg 1.4956199E-03 0.1755338 1,midg,midg; igrid,midg,midg -3.8663574E-02 -8.3972268E-02 gauss-seidel spectral radius is 0.9991170 estimated iterations to convergence 266 setup time was (sec) 1.380000 now iterating at: 03:15:04 rms-change max change #iterations 8.688533 283.2451 at 10iterations 4.850226 123.5361 at 20iterations 2.682452 64.12877 at 30iterations 1.482928 35.82018 at 40iterations 0.8159688 18.06019 at 50iterations 0.4483604 10.28254 at 60iterations 0.2459748 6.310753 at 70iterations 0.1344482 2.702839 at 80iterations 7.3566996E-02 1.835388 at 90iterations 4.0142767E-02 0.8190139 at 100iterations 2.1901641E-02 0.4344158 at 110iterations 1.1960088E-02 0.2518196 at 120iterations 6.5235831E-03 0.1513901 at 130iterations 3.5722195E-03 7.6843262E-02 at 140iterations 1.9473716E-03 3.6926270E-02 at 150iterations 1.0631026E-03 2.2727013E-02 at 160iterations 5.8336434E-04 1.1596680E-02 at 170iterations 3.2040122E-04 7.1544647E-03 at 180iterations finished qdiffx linear iterations at : 03:15:14 total time elapsed so far: 11.47000 # loops : 180 mean,max change (kT/e) : 3.2040122E-04 7.1544647E-03 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 03:15:15 11.642u 0.246s 0:12.46 95.3% 0+0k 0+0io 0pf+0w