Sat Oct 8 19:05:32 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 19:05:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6211180 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 0.6211180 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 88.67032 89.14158 89.92496 assigned negative charge : -388.8705 centred at (gu) : 88.57136 89.18555 89.81457 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 52819 no. pairs analyzed = 52819 no. exposed pairs = 3102 no. arc points = 21977 no. surface atoms = 1053 nbur = 1541 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3809 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1900000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9108858E-09 1.1123274E-08 midg,1,midg; midg,igrid,midg 8.2406881E-09 6.8797418E-10 1,midg,midg; igrid,midg,midg -4.1872319E-09 7.8877855E-09 gauss-seidel spectral radius is 0.9865768 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 19:05:33 rms-change max change #iterations 0.1269649 19.82598 at 10iterations 1.1921372E-02 1.770353 at 20iterations 1.1468135E-03 0.1633911 at 30iterations 1.1080143E-04 1.8325806E-02 at 40iterations 1.1434143E-05 1.6479492E-03 at 50iterations finished qdiffx linear iterations at : 19:05:36 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.1434143E-05 1.6479492E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 19:05:36 3.341u 0.174s 0:03.83 91.6% 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 19:05:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.863354 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 1.863354 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 86.01067 87.42461 89.77455 assigned negative charge : -388.8705 centred at (gu) : 85.71389 87.55651 89.44369 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21977 grid for indexing accessible points = 1.400000 m= 27060 mr = 50902 m= 4095 mr = 20336 m= 189 mr = 2488 m= 0 mr = 43 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 869 time to turn everything in is 0.3500000 number of dielectric boundary points 30278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19292 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) : 0.6211180 object centre at (A) : -7.507999 -0.7205000 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8261625E-02 2.6216125E-02 midg,1,midg; midg,igrid,midg 1.6303606E-02 2.3238808E-03 1,midg,midg; igrid,midg,midg -2.8410519E-03 3.5022527E-02 gauss-seidel spectral radius is 0.9985763 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 19:05:37 rms-change max change #iterations 4.065119 187.3190 at 10iterations 1.872199 63.86041 at 20iterations 0.8639677 29.33759 at 30iterations 0.3967042 12.45870 at 40iterations 0.1830385 5.657478 at 50iterations 8.4447041E-02 2.537308 at 60iterations 3.9001696E-02 1.279923 at 70iterations 1.7982025E-02 0.5633888 at 80iterations 8.2732970E-03 0.3035240 at 90iterations 3.8206999E-03 0.1278896 at 100iterations 1.7632204E-03 5.4580688E-02 at 110iterations 8.1751263E-04 2.6876450E-02 at 120iterations finished qdiffx linear iterations at : 19:05:44 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 8.1751263E-04 2.6876450E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 19:05:44 7.681u 0.188s 0:08.13 96.6% 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 19:05:44 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.795031 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 2.795031 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 393.3700 centred at (gu) : 84.01601 86.13671 89.66177 assigned negative charge : -388.8705 centred at (gu) : 83.57076 86.33477 89.16537 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 168116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21977 grid for indexing accessible points = 1.400000 m= 86948 mr = 122914 m= 31882 mr = 72143 m= 7293 mr = 25852 m= 915 mr = 5332 m= 28 mr = 529 m= 0 mr = 5 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2812 time to turn everything in is 0.9100000 number of dielectric boundary points 68407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19691 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) : 1.863354 object centre at (A) : -7.507999 -0.7205000 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6702902E-02 0.3119891 midg,1,midg; midg,igrid,midg 0.1851539 2.2364182E-02 1,midg,midg; igrid,midg,midg -1.6797196E-02 0.4399668 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.140000 now iterating at: 19:05:46 rms-change max change #iterations 9.530940 353.1763 at 10iterations 5.480618 126.5899 at 20iterations 3.144078 59.88889 at 30iterations 1.801060 34.16699 at 40iterations 1.031722 18.94199 at 50iterations 0.5871695 11.78665 at 60iterations 0.3352982 6.855408 at 70iterations 0.1910162 3.636779 at 80iterations 0.1088626 2.047390 at 90iterations 6.1962802E-02 1.174696 at 100iterations 3.5352264E-02 0.6988306 at 110iterations 2.0152133E-02 0.3920212 at 120iterations 1.1485937E-02 0.2478161 at 130iterations 6.5484140E-03 0.1196938 at 140iterations 3.7346527E-03 6.7676544E-02 at 150iterations 2.1342281E-03 3.7550449E-02 at 160iterations 1.2199628E-03 2.2155762E-02 at 170iterations 7.0055801E-04 1.3977051E-02 at 180iterations finished qdiffx linear iterations at : 19:05:57 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 7.0055801E-04 1.3977051E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 19:05:57 12.379u 0.208s 0:12.86 97.7% 0+0k 0+0io 0pf+0w