Tue Oct 11 03:23:32 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 Tue Oct 11 2011 at 03:23:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6067941 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): -26.25300 23.93900 ymin,ymax (A): -52.17300 -8.653999 zmin,zma (A): -30.34700 28.32200 x,y,z range (A): 50.19200 43.51900 58.66900 scale (grids/A): 0.6067941 object centre (A): -1.157000 -30.41350 -1.012500 number of atom coordinates read : 2221 total number of charged atoms : 2076 net assigned charge : 5.9902668E-06 assigned positive charge : 322.6895 centred at (gu) : 91.98463 89.69817 90.17966 assigned negative charge : -322.6900 centred at (gu) : 92.07913 89.73512 90.12540 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 44325 no. pairs analyzed = 44325 no. exposed pairs = 3026 no. arc points = 21456 no. surface atoms = 1008 nbur = 1213 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 254 mr = 2896 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2101 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8794086E-09 2.1647957E-09 midg,1,midg; midg,igrid,midg 1.5432815E-09 -1.2204416E-09 1,midg,midg; igrid,midg,midg 2.2652766E-09 -5.5141993E-09 gauss-seidel spectral radius is 0.9859156 estimated iterations to convergence 69 setup time was (sec) 0.3500000 now iterating at: 03:23:32 rms-change max change #iterations 0.1058392 19.33451 at 10iterations 8.9871194E-03 1.718607 at 20iterations 8.0728560E-04 0.1297188 at 30iterations 8.1798506E-05 1.6002655E-02 at 40iterations 1.2280924E-05 2.7122498E-03 at 50iterations finished qdiffx linear iterations at : 03:23:35 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.2280924E-05 2.7122498E-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) 3.330000 DelPhi exited at 03:23:35 3.332u 0.176s 0:03.80 92.1% 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 03:23:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.820382 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): -26.25300 23.93900 ymin,ymax (A): -52.17300 -8.653999 zmin,zma (A): -30.34700 28.32200 x,y,z range (A): 50.19200 43.51900 58.66900 scale (grids/A): 1.820382 object centre (A): -1.157000 -30.41350 -1.012500 number of atom coordinates read : 2221 total number of charged atoms : 2076 net assigned charge : 5.9902668E-06 assigned positive charge : 322.6895 centred at (gu) : 95.95361 89.09404 90.53872 assigned negative charge : -322.6900 centred at (gu) : 96.23734 89.20533 90.37604 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21456 grid for indexing accessible points = 1.400000 m= 19839 mr = 40538 m= 2387 mr = 13705 m= 123 mr = 1192 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 298 time to turn everything in is 0.3000000 number of dielectric boundary points 27764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 16252 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) : 0.6067941 object centre at (A) : -1.157000 -30.41350 -1.012500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4837345E-02 -5.5816229E-03 midg,1,midg; midg,igrid,midg 4.1892878E-03 -7.6651452E-03 1,midg,midg; igrid,midg,midg 1.2811956E-02 -2.7667813E-03 gauss-seidel spectral radius is 0.9984719 estimated iterations to convergence 203 setup time was (sec) 0.5000000 now iterating at: 03:23:36 rms-change max change #iterations 3.503352 166.6492 at 10iterations 1.557417 61.38370 at 20iterations 0.6965633 23.78085 at 30iterations 0.3118935 11.63156 at 40iterations 0.1400855 4.806992 at 50iterations 6.2473718E-02 2.091755 at 60iterations 2.7852522E-02 0.9969540 at 70iterations 1.2528512E-02 0.4654980 at 80iterations 5.6038029E-03 0.2041569 at 90iterations 2.5178397E-03 8.2975388E-02 at 100iterations 1.1277817E-03 4.1854858E-02 at 110iterations 5.0990452E-04 1.8275261E-02 at 120iterations finished qdiffx linear iterations at : 03:23:43 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 5.0990452E-04 1.8275261E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 03:23:44 7.616u 0.205s 0:08.13 96.0% 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 Tue Oct 11 2011 at 03:23:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.730573 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): -26.25300 23.93900 ymin,ymax (A): -52.17300 -8.653999 zmin,zma (A): -30.34700 28.32200 x,y,z range (A): 50.19200 43.51900 58.66900 scale (grids/A): 2.730573 object centre (A): -1.157000 -30.41350 -1.012500 number of atom coordinates read : 2221 total number of charged atoms : 2076 net assigned charge : 5.9902668E-06 assigned positive charge : 322.6895 centred at (gu) : 98.93037 88.64124 90.80791 assigned negative charge : -322.6900 centred at (gu) : 99.35590 88.80804 90.56397 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 140987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21456 grid for indexing accessible points = 1.400000 m= 66622 mr = 98854 m= 21055 mr = 52992 m= 4043 mr = 15839 m= 455 mr = 2649 m= 27 mr = 203 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1052 time to turn everything in is 0.7600000 number of dielectric boundary points 62647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 16602 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) : 1.820382 object centre at (A) : -1.157000 -30.41350 -1.012500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3367517 3.9537877E-02 midg,1,midg; midg,igrid,midg 4.8952203E-02 -0.1067926 1,midg,midg; igrid,midg,midg 0.1562698 -3.3890892E-02 gauss-seidel spectral radius is 0.9992103 estimated iterations to convergence 281 setup time was (sec) 1.000000 now iterating at: 03:23:45 rms-change max change #iterations 8.470618 271.3550 at 10iterations 4.890380 118.5244 at 20iterations 2.801651 61.85617 at 30iterations 1.595836 34.71435 at 40iterations 0.9059791 19.48366 at 50iterations 0.5128269 11.50375 at 60iterations 0.2916831 6.873557 at 70iterations 0.1649796 3.455204 at 80iterations 9.3246378E-02 2.155903 at 90iterations 5.2731089E-02 1.179205 at 100iterations 2.9855652E-02 0.6028824 at 110iterations 1.6854316E-02 0.3630095 at 120iterations 9.5399022E-03 0.1988719 at 130iterations 5.3720595E-03 0.1379166 at 140iterations 3.0460046E-03 6.2583923E-02 at 150iterations 1.7272121E-03 3.7609100E-02 at 160iterations 9.8463008E-04 2.3296356E-02 at 170iterations 5.6734745E-04 1.2314796E-02 at 180iterations finished qdiffx linear iterations at : 03:23:56 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 5.6734745E-04 1.2314796E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 03:23:56 12.123u 0.192s 0:12.62 97.5% 0+0k 0+0io 0pf+0w