Sat Oct 15 11:46:04 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 15 2011 at 11:46:04 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 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: 0.4958839 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): -82.47900 -10.68800 ymin,ymax (A): -16.60000 41.75300 zmin,zma (A): -57.13200 13.56500 x,y,z range (A): 71.79100 58.35300 70.69700 scale (grids/A): 0.4958839 object centre (A): -46.58350 12.57650 -21.78350 number of atom coordinates read : 4328 total number of charged atoms : 4167 net assigned charge : 14.50001 assigned positive charge : 659.8901 centred at (gu) : 89.96959 91.29517 90.25980 assigned negative charge : -645.3934 centred at (gu) : 89.97206 91.23618 90.19539 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6831 nv = 96 ne = 84 npr = 83720 no. pairs analyzed = 83720 no. exposed pairs = 5850 no. arc points = 41589 no. surface atoms = 1967 nbur = 2361 mkacc time = 0.1500000 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= 246 mr = 3147 m= 0 mr = 1 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4106 ## 667 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2344189E-11 1.9461180E-10 midg,1,midg; midg,igrid,midg 2.2475037E-11 2.4823921E-10 1,midg,midg; igrid,midg,midg 1.0716769E-10 9.9457415E-11 gauss-seidel spectral radius is 0.9791886 estimated iterations to convergence 57 setup time was (sec) 0.5000000 now iterating at: 11:46:04 rms-change max change #iterations 5.3940602E-02 9.012913 at 10iterations 3.0462709E-03 0.5445175 at 20iterations 3.2910614E-04 5.4748535E-02 at 30iterations 7.7219040E-05 1.3732910E-02 at 40iterations 2.0154090E-05 3.6392212E-03 at 50iterations finished qdiffx linear iterations at : 11:46:07 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 2.0154090E-05 3.6392212E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 11:46:08 3.759u 0.211s 0:04.40 90.0% 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 15 2011 at 11:46:08 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 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: 1.487652 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): -82.47900 -10.68800 ymin,ymax (A): -16.60000 41.75300 zmin,zma (A): -57.13200 13.56500 x,y,z range (A): 71.79100 58.35300 70.69700 scale (grids/A): 1.487652 object centre (A): -46.58350 12.57650 -21.78350 number of atom coordinates read : 4328 total number of charged atoms : 4167 net assigned charge : 14.50001 assigned positive charge : 659.8901 centred at (gu) : 89.90778 93.88433 90.77769 assigned negative charge : -645.3934 centred at (gu) : 89.91601 93.70820 90.58577 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 76908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 20787 mr = 49711 m= 1674 mr = 12474 m= 38 mr = 546 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 36678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 606 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 30990 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) : 0.4958839 object centre at (A) : -46.58350 12.57650 -21.78350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9890648E-03 2.1368977E-02 midg,1,midg; midg,igrid,midg 8.0179895E-04 1.2850637E-02 1,midg,midg; igrid,midg,midg 2.9471540E-03 1.4312975E-03 gauss-seidel spectral radius is 0.9979378 estimated iterations to convergence 175 setup time was (sec) 0.6400000 now iterating at: 11:46:09 rms-change max change #iterations 3.340136 162.5276 at 10iterations 1.305357 46.10406 at 20iterations 0.5118442 21.29352 at 30iterations 0.2009856 7.781273 at 40iterations 7.9262175E-02 2.735083 at 50iterations 3.1173123E-02 1.190323 at 60iterations 1.2340197E-02 0.5384407 at 70iterations 4.8424015E-03 0.1587243 at 80iterations 1.9132276E-03 6.7198753E-02 at 90iterations 7.5986987E-04 2.7014256E-02 at 100iterations 3.0374603E-04 1.2661457E-02 at 110iterations 1.2449110E-04 5.2051544E-03 at 120iterations finished qdiffx linear iterations at : 11:46:16 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 1.2449110E-04 5.2051544E-03 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 11:46:17 8.364u 0.232s 0:09.06 94.8% 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 Sat Oct 15 2011 at 11:46:17 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 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: 2.231477 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): -82.47900 -10.68800 ymin,ymax (A): -16.60000 41.75300 zmin,zma (A): -57.13200 13.56500 x,y,z range (A): 71.79100 58.35300 70.69700 scale (grids/A): 2.231477 object centre (A): -46.58350 12.57650 -21.78350 number of atom coordinates read : 4328 total number of charged atoms : 4167 net assigned charge : 14.50001 assigned positive charge : 659.8901 centred at (gu) : 89.86125 95.82608 91.16654 assigned negative charge : -645.3934 centred at (gu) : 89.87382 95.56200 90.87860 start vw surface at 0.1200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 179299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41589 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 75462 mr = 123556 m= 17305 mr = 55688 m= 2157 mr = 11169 m= 94 mr = 1062 m= 0 mr = 17 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 82825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 33196 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) : 1.487652 object centre at (A) : -46.58350 12.57650 -21.78350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1360486 0.5118821 midg,1,midg; midg,igrid,midg -3.0198593E-02 0.1808928 1,midg,midg; igrid,midg,midg 0.1913772 -0.3471462 gauss-seidel spectral radius is 0.9990974 estimated iterations to convergence 263 setup time was (sec) 1.200000 now iterating at: 11:46:19 rms-change max change #iterations 9.385192 269.0888 at 10iterations 5.295583 137.4176 at 20iterations 2.964831 79.46702 at 30iterations 1.647244 38.73727 at 40iterations 0.9078740 19.40082 at 50iterations 0.5004653 11.97126 at 60iterations 0.2741119 6.368464 at 70iterations 0.1500149 3.291718 at 80iterations 8.1971392E-02 1.841540 at 90iterations 4.4630565E-02 0.8958006 at 100iterations 2.4341408E-02 0.5600171 at 110iterations 1.3197722E-02 0.2911987 at 120iterations 7.1938303E-03 0.1587830 at 130iterations 3.9006213E-03 7.7718735E-02 at 140iterations 2.1204404E-03 4.2316437E-02 at 150iterations 1.1498345E-03 2.2202611E-02 at 160iterations 6.2357303E-04 1.3836384E-02 at 170iterations 3.3842798E-04 7.2169304E-03 at 180iterations finished qdiffx linear iterations at : 11:46:43 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 3.3842798E-04 7.2169304E-03 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 11:46:44 13.260u 0.236s 0:26.53 50.8% 0+0k 0+0io 0pf+0w