Sun Oct 9 10:14:48 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 Sun Oct 9 2011 at 10:14:48 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 = 2043 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: 0.6537748 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 0.6537748 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.000015 assigned positive charge : 302.7538 centred at (gu) : 89.61525 91.03031 89.82847 assigned negative charge : -299.7543 centred at (gu) : 89.55784 91.03127 89.85693 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6035 nv = 96 ne = 84 npr = 40512 no. pairs analyzed = 40512 no. exposed pairs = 2672 no. arc points = 18660 no. surface atoms = 901 nbur = 1142 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3293 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0512498E-08 2.6592963E-09 midg,1,midg; midg,igrid,midg 5.3482170E-09 7.8087306E-09 1,midg,midg; igrid,midg,midg -1.1746155E-09 1.2805804E-08 gauss-seidel spectral radius is 0.9878304 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 10:14:49 rms-change max change #iterations 0.1370185 23.45947 at 10iterations 1.4157602E-02 1.983080 at 20iterations 1.4709847E-03 0.2274876 at 30iterations 1.5300486E-04 2.2906303E-02 at 40iterations 1.5855654E-05 2.3422241E-03 at 50iterations finished qdiffx linear iterations at : 10:14:52 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.5855654E-05 2.3422241E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 10:14:52 3.403u 0.185s 0:03.86 92.7% 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 10:14:52 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 = 2043 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: 1.961324 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 1.961324 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.000015 assigned positive charge : 302.7538 centred at (gu) : 88.84549 93.09062 89.48528 assigned negative charge : -299.7543 centred at (gu) : 88.67380 93.09406 89.57101 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18660 grid for indexing accessible points = 1.400000 m= 23571 mr = 44379 m= 4191 mr = 17258 m= 303 mr = 2684 m= 4 mr = 158 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 344 time to turn everything in is 0.3700000 number of dielectric boundary points 28398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15574 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) : 0.6537748 object centre at (A) : 18.98950 27.16250 15.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0202532E-03 7.5491477E-04 midg,1,midg; midg,igrid,midg 3.1854589E-02 3.2217097E-02 1,midg,midg; igrid,midg,midg -2.4970383E-03 -1.1511329E-03 gauss-seidel spectral radius is 0.9986626 estimated iterations to convergence 217 setup time was (sec) 0.5900000 now iterating at: 10:14:53 rms-change max change #iterations 3.886710 169.6105 at 10iterations 1.835004 62.85585 at 20iterations 0.8605469 28.70897 at 30iterations 0.4061528 13.32625 at 40iterations 0.1926292 6.026727 at 50iterations 9.0570547E-02 2.997583 at 60iterations 4.2781811E-02 1.437397 at 70iterations 2.0227892E-02 0.6268735 at 80iterations 9.5712552E-03 0.3129873 at 90iterations 4.5071123E-03 0.1444941 at 100iterations 2.1311201E-03 6.8714619E-02 at 110iterations 1.0065386E-03 3.4274101E-02 at 120iterations finished qdiffx linear iterations at : 10:15:01 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.0065386E-03 3.4274101E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 10:15:01 7.742u 1.123s 0:09.33 94.9% 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 10:15:01 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 = 2043 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: 2.941987 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 2.941987 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.000015 assigned positive charge : 302.7538 centred at (gu) : 88.26814 94.63589 89.22791 assigned negative charge : -299.7543 centred at (gu) : 88.01067 94.64118 89.35645 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 149672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18660 grid for indexing accessible points = 1.400000 m= 74879 mr = 107740 m= 28793 mr = 60644 m= 7667 mr = 23257 m= 1288 mr = 5782 m= 113 mr = 935 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.9100000 number of dielectric boundary points 63975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 15776 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) : 1.961324 object centre at (A) : 18.98950 27.16250 15.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9526865E-02 0.1062319 midg,1,midg; midg,igrid,midg 0.3491903 0.2636845 1,midg,midg; igrid,midg,midg -3.3087350E-02 -4.1233074E-02 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 1.160000 now iterating at: 10:15:03 rms-change max change #iterations 9.056188 399.2400 at 10iterations 5.277011 129.0757 at 20iterations 3.069495 75.68797 at 30iterations 1.784235 36.89614 at 40iterations 1.032641 20.29781 at 50iterations 0.5971193 11.07998 at 60iterations 0.3446932 6.773488 at 70iterations 0.1987936 3.726057 at 80iterations 0.1148664 2.384973 at 90iterations 6.6084959E-02 1.233080 at 100iterations 3.8110819E-02 0.7539387 at 110iterations 2.1932837E-02 0.4720230 at 120iterations 1.2626368E-02 0.2405663 at 130iterations 7.2559346E-03 0.1499262 at 140iterations 4.1775424E-03 8.3129883E-02 at 150iterations 2.4009917E-03 4.4570923E-02 at 160iterations 1.3827803E-03 2.6721358E-02 at 170iterations 7.9665147E-04 1.4645815E-02 at 180iterations finished qdiffx linear iterations at : 10:15:14 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 7.9665147E-04 1.4645815E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 10:15:15 12.732u 0.259s 0:13.50 96.1% 0+0k 0+0io 0pf+0w