Sat Oct 8 18:26:40 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 Sat Oct 8 2011 at 18:26:40 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 = 3325 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: 0.5568068 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 0.5568068 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 496.8985 centred at (gu) : 89.66993 90.90258 90.24512 assigned negative charge : -490.3999 centred at (gu) : 89.83782 90.95084 90.25931 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7036 nv = 96 ne = 84 npr = 64896 no. pairs analyzed = 64896 no. exposed pairs = 4557 no. arc points = 33174 no. surface atoms = 1504 nbur = 1821 mkacc time = 0.1900000 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 = 1.568000 m= 339 mr = 3480 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3292 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2466139E-10 4.8581694E-10 midg,1,midg; midg,igrid,midg 9.1556934E-10 9.7618337E-11 1,midg,midg; igrid,midg,midg 2.6088958E-09 -1.1542952E-09 gauss-seidel spectral radius is 0.9834055 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 18:26:41 rms-change max change #iterations 8.1202261E-02 14.03725 at 10iterations 6.0961684E-03 0.8637466 at 20iterations 6.5808726E-04 9.6412659E-02 at 30iterations 1.3289614E-04 1.9386292E-02 at 40iterations 3.2706768E-05 4.8446655E-03 at 50iterations finished qdiffx linear iterations at : 18:26:44 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.2706768E-05 4.8446655E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 18:26:45 4.136u 0.273s 0:04.68 94.0% 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 Sat Oct 8 2011 at 18:26:45 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 = 3325 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: 1.670420 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 1.670420 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 496.8985 centred at (gu) : 89.00874 92.70663 90.73430 assigned negative charge : -490.3999 centred at (gu) : 89.51337 92.85239 90.77725 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33174 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24510 mr = 50590 m= 2860 mr = 16388 m= 98 mr = 1400 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 706 time to turn everything in is 0.6800000 number of dielectric boundary points 35915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 24440 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) : 0.5568068 object centre at (A) : 10.04700 25.75500 37.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1991657E-03 -4.6429341E-03 midg,1,midg; midg,igrid,midg 2.8504322E-03 3.7240650E-04 1,midg,midg; igrid,midg,midg 1.6483076E-02 -1.2215768E-02 gauss-seidel spectral radius is 0.9983258 estimated iterations to convergence 194 setup time was (sec) 0.9700000 now iterating at: 18:26:46 rms-change max change #iterations 3.716412 215.5644 at 10iterations 1.592199 55.15556 at 20iterations 0.6845205 23.88371 at 30iterations 0.2955590 10.54176 at 40iterations 0.1282378 4.206236 at 50iterations 5.5093054E-02 1.854208 at 60iterations 2.3788761E-02 0.8652191 at 70iterations 1.0272194E-02 0.3521423 at 80iterations 4.4633285E-03 0.1502185 at 90iterations 1.9372420E-03 6.1035156E-02 at 100iterations 8.4845588E-04 2.6283264E-02 at 110iterations 3.7768568E-04 1.2336731E-02 at 120iterations finished qdiffx linear iterations at : 18:26:55 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 3.7768568E-04 1.2336731E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 18:26:55 9.492u 0.303s 0:10.06 97.3% 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 Sat Oct 8 2011 at 18:26:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3325 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: 2.505630 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): -19.80900 39.90300 ymin,ymax (A): -2.182000 53.69200 zmin,zma (A): 5.287000 69.22300 x,y,z range (A): 59.71200 55.87400 63.93600 scale (grids/A): 2.505630 object centre (A): 10.04700 25.75500 37.25500 number of atom coordinates read : 3325 total number of charged atoms : 3181 net assigned charge : 6.500046 assigned positive charge : 496.8985 centred at (gu) : 88.51286 94.05952 91.10117 assigned negative charge : -490.3999 centred at (gu) : 89.27003 94.27844 91.16589 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 178196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33174 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 82699 mr = 124030 m= 25167 mr = 64092 m= 4556 mr = 18676 m= 353 mr = 2898 m= 7 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2445 time to turn everything in is 1.700000 number of dielectric boundary points 81161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 25427 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) : 1.670420 object centre at (A) : 10.04700 25.75500 37.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1121792 -0.2393514 midg,1,midg; midg,igrid,midg -2.1490816E-02 9.5789142E-02 1,midg,midg; igrid,midg,midg 0.1876065 -0.1758327 gauss-seidel spectral radius is 0.9991974 estimated iterations to convergence 279 setup time was (sec) 2.040000 now iterating at: 18:26:57 rms-change max change #iterations 9.597540 371.0417 at 10iterations 5.601345 137.0185 at 20iterations 3.236161 73.74902 at 30iterations 1.853376 41.41829 at 40iterations 1.058703 23.56524 at 50iterations 0.6026964 13.83517 at 60iterations 0.3414252 7.436213 at 70iterations 0.1939263 4.128516 at 80iterations 0.1093442 2.140866 at 90iterations 6.1875451E-02 1.371409 at 100iterations 3.4862477E-02 0.7553511 at 110iterations 1.9656567E-02 0.4467568 at 120iterations 1.1068146E-02 0.2823944 at 130iterations 6.2469202E-03 0.1146545 at 140iterations 3.5069094E-03 6.7049026E-02 at 150iterations 1.9703996E-03 4.2926788E-02 at 160iterations 1.1082091E-03 2.2033691E-02 at 170iterations 6.2400283E-04 1.2354612E-02 at 180iterations finished qdiffx linear iterations at : 18:27:11 total time elapsed so far: 15.81000 # loops : 180 mean,max change (kT/e) : 6.2400283E-04 1.2354612E-02 energy calculations done at 15.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 18:27:12 15.984u 0.311s 0:16.55 98.4% 0+0k 0+0io 0pf+0w