Sun Oct 9 21:17:53 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 21:17:53 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 0.6091301 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 0.6091301 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3136 net assigned charge : 5.025015 assigned positive charge : 499.4286 centred at (gu) : 90.24495 87.57275 90.63223 assigned negative charge : -494.4049 centred at (gu) : 90.16167 87.49033 90.63745 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8162 nv = 96 ne = 84 npr = 59246 no. pairs analyzed = 59246 no. exposed pairs = 4397 no. arc points = 32181 no. surface atoms = 1448 nbur = 1745 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4109 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.4000000 number of dielectric boundary points 4470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3258 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8874938E-09 3.0682625E-09 midg,1,midg; midg,igrid,midg -3.7913210E-09 4.6666742E-09 1,midg,midg; igrid,midg,midg -2.0060766E-09 8.4747338E-09 gauss-seidel spectral radius is 0.9861150 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 21:17:54 rms-change max change #iterations 0.1282586 17.72133 at 10iterations 1.1233486E-02 1.731522 at 20iterations 1.0112398E-03 0.1370921 at 30iterations 9.5475341E-05 1.2752533E-02 at 40iterations 1.2887115E-05 1.7704964E-03 at 50iterations finished qdiffx linear iterations at : 21:17:57 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.2887115E-05 1.7704964E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 21:17:58 4.113u 0.254s 0:04.64 93.9% 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 21:17:58 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 1.827390 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 1.827390 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3136 net assigned charge : 5.025015 assigned positive charge : 499.4286 centred at (gu) : 90.73434 82.71724 91.89561 assigned negative charge : -494.4049 centred at (gu) : 90.48438 82.47074 91.91193 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32181 grid for indexing accessible points = 1.400000 m= 29918 mr = 57973 m= 4281 mr = 20585 m= 237 mr = 2355 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1541 time to turn everything in is 0.7700000 number of dielectric boundary points 41386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 24529 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) : 0.6091301 object centre at (A) : 71.82249 32.40300 41.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2187494E-03 -2.1700703E-03 midg,1,midg; midg,igrid,midg 3.7046682E-02 2.7861614E-02 1,midg,midg; igrid,midg,midg -1.2482926E-02 1.3166020E-02 gauss-seidel spectral radius is 0.9986036 estimated iterations to convergence 212 setup time was (sec) 1.070000 now iterating at: 21:17:59 rms-change max change #iterations 4.469732 178.4964 at 10iterations 2.070520 66.03346 at 20iterations 0.9574116 30.80541 at 30iterations 0.4420083 14.72844 at 40iterations 0.2048721 6.489120 at 50iterations 9.4913021E-02 2.868686 at 60iterations 4.3798409E-02 1.440845 at 70iterations 2.0361690E-02 0.6326027 at 80iterations 9.4419383E-03 0.2875099 at 90iterations 4.3828823E-03 0.1369958 at 100iterations 2.0271987E-03 5.9246063E-02 at 110iterations 9.4485446E-04 2.8320313E-02 at 120iterations finished qdiffx linear iterations at : 21:18:07 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 9.4485446E-04 2.8320313E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 21:18:08 9.654u 0.300s 0:10.27 96.8% 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 21:18:08 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 2.741086 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 2.741086 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3136 net assigned charge : 5.025015 assigned positive charge : 499.4286 centred at (gu) : 91.10125 79.07557 92.84313 assigned negative charge : -494.4049 centred at (gu) : 90.72646 78.70607 92.86777 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 203705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32181 grid for indexing accessible points = 1.400000 m= 97763 mr = 141720 m= 33111 mr = 76919 m= 7442 mr = 25279 m= 1009 mr = 5150 m= 63 mr = 645 m= 0 mr = 24 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 5574 time to turn everything in is 1.960000 number of dielectric boundary points 93356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 25085 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) : 1.827390 object centre at (A) : 71.82249 32.40300 41.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8725213E-02 -0.1523748 midg,1,midg; midg,igrid,midg 0.3192709 0.3298924 1,midg,midg; igrid,midg,midg -0.1733309 0.1669370 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.290000 now iterating at: 21:18:11 rms-change max change #iterations 10.91220 309.1395 at 10iterations 6.543266 151.8650 at 20iterations 3.874009 106.5402 at 30iterations 2.280803 68.72311 at 40iterations 1.340832 29.55631 at 50iterations 0.7860450 15.78515 at 60iterations 0.4585871 9.278083 at 70iterations 0.2676763 5.093837 at 80iterations 0.1555058 2.907413 at 90iterations 9.0521477E-02 1.701385 at 100iterations 5.2643526E-02 0.9318719 at 110iterations 3.0598493E-02 0.5971909 at 120iterations 1.7764620E-02 0.3134098 at 130iterations 1.0326396E-02 0.1787586 at 140iterations 5.9871185E-03 0.1161728 at 150iterations 3.4730909E-03 5.8782578E-02 at 160iterations 2.0141646E-03 3.6693573E-02 at 170iterations 1.1672697E-03 2.1330833E-02 at 180iterations finished qdiffx linear iterations at : 21:18:25 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 1.1672697E-03 2.1330833E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.63000 DelPhi exited at 21:18:25 16.635u 0.310s 0:17.21 98.4% 0+0k 0+0io 0pf+0w