Tue Oct 11 03:45:55 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 03:45:55 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIR 79 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6716855 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 0.6716855 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.514015 assigned positive charge : 412.4318 centred at (gu) : 89.89819 90.02723 91.01994 assigned negative charge : -407.9184 centred at (gu) : 89.64683 89.84603 90.99297 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8269 nv = 96 ne = 84 npr = 55273 no. pairs analyzed = 55273 no. exposed pairs = 3237 no. arc points = 22359 no. surface atoms = 1093 nbur = 1622 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 543 mr = 4829 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3500000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8114185E-09 2.8613908E-08 midg,1,midg; midg,igrid,midg -3.5526323E-08 6.5736252E-08 1,midg,midg; igrid,midg,midg -5.7443820E-08 8.2324917E-08 gauss-seidel spectral radius is 0.9885164 estimated iterations to convergence 76 setup time was (sec) 0.6000000 now iterating at: 03:45:56 rms-change max change #iterations 0.1884778 27.20760 at 10iterations 2.0759927E-02 2.692909 at 20iterations 2.3427373E-03 0.2876434 at 30iterations 2.6248721E-04 3.1799316E-02 at 40iterations 3.0931275E-05 4.0836334E-03 at 50iterations finished qdiffx linear iterations at : 03:45:59 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.0931275E-05 4.0836334E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:45:59 3.428u 0.167s 0:04.00 89.5% 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 03:45:59 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIR 79 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.015056 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 2.015056 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.514015 assigned positive charge : 412.4318 centred at (gu) : 89.69431 90.08109 93.05939 assigned negative charge : -407.9184 centred at (gu) : 88.94020 89.53780 92.97878 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22359 grid for indexing accessible points = 1.400000 m= 35896 mr = 63568 m= 6921 mr = 27698 m= 565 mr = 4638 m= 8 mr = 265 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1882 time to turn everything in is 0.6800000 number of dielectric boundary points 35704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20318 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) : 0.6716855 object centre at (A) : 13.59400 -2.494499 19.19250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5085726E-02 6.2015727E-03 midg,1,midg; midg,igrid,midg -1.1217599E-02 5.3290214E-02 1,midg,midg; igrid,midg,midg -1.3105458E-02 8.0588840E-02 gauss-seidel spectral radius is 0.9987841 estimated iterations to convergence 227 setup time was (sec) 0.9600000 now iterating at: 03:46:01 rms-change max change #iterations 4.890492 197.3157 at 10iterations 2.404111 72.06588 at 20iterations 1.175961 33.78655 at 30iterations 0.5755417 16.22699 at 40iterations 0.2824093 8.258545 at 50iterations 0.1385712 4.187433 at 60iterations 6.7858353E-02 2.061306 at 70iterations 3.3214174E-02 1.082622 at 80iterations 1.6300485E-02 0.4444809 at 90iterations 7.9666916E-03 0.2086473 at 100iterations 3.9159623E-03 0.1069603 at 110iterations 1.9163893E-03 5.4623127E-02 at 120iterations finished qdiffx linear iterations at : 03:46:07 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.9163893E-03 5.4623127E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 03:46:08 7.896u 0.206s 0:08.70 92.9% 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 Tue Oct 11 2011 at 03:46:08 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 !!! WARNING: HIR 79 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.022584 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 3.022584 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.514015 assigned positive charge : 412.4318 centred at (gu) : 89.54115 90.12142 94.58886 assigned negative charge : -407.9184 centred at (gu) : 88.41023 89.30655 94.46805 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 203873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22359 grid for indexing accessible points = 1.400000 m= 111970 mr = 152748 m= 46006 mr = 93860 m= 12831 mr = 38220 m= 2367 mr = 10057 m= 234 mr = 1768 m= 7 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 6238 time to turn everything in is 1.750000 number of dielectric boundary points 80505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 20544 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) : 2.015056 object centre at (A) : 13.59400 -2.494499 19.19250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2913743 0.2617463 midg,1,midg; midg,igrid,midg -0.1274110 0.5579262 1,midg,midg; igrid,midg,midg -5.2805286E-02 0.6846118 gauss-seidel spectral radius is 0.9992938 estimated iterations to convergence 297 setup time was (sec) 2.050000 now iterating at: 03:46:10 rms-change max change #iterations 11.10768 372.6243 at 10iterations 6.568308 157.2247 at 20iterations 3.874907 88.15182 at 30iterations 2.276928 39.15181 at 40iterations 1.336670 24.83708 at 50iterations 0.7838818 13.99469 at 60iterations 0.4597580 9.555395 at 70iterations 0.2688993 4.689316 at 80iterations 0.1573280 2.515181 at 90iterations 9.1943860E-02 1.523849 at 100iterations 5.3672131E-02 0.8958941 at 110iterations 3.1400736E-02 0.5637693 at 120iterations 1.8335855E-02 0.3063097 at 130iterations 1.0730500E-02 0.1859646 at 140iterations 6.2807105E-03 0.1011572 at 150iterations 3.6785826E-03 6.3518524E-02 at 160iterations 2.1654537E-03 3.7399292E-02 at 170iterations 1.2813160E-03 2.1928787E-02 at 180iterations finished qdiffx linear iterations at : 03:46:21 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 1.2813160E-03 2.1928787E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 03:46:21 12.538u 0.222s 0:13.18 96.7% 0+0k 0+0io 0pf+0w