Sat Oct 8 21:42:41 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 Sat Oct 8 2011 at 21:42:41 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2055 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6667041 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): 5.451000 58.84800 ymin,ymax (A): 2.811000 49.81900 zmin,zma (A): 13.38600 55.87300 x,y,z range (A): 53.39700 47.00800 42.48700 scale (grids/A): 0.6667041 object centre (A): 32.14950 26.31500 34.62950 number of atom coordinates read : 2055 total number of charged atoms : 1915 net assigned charge : 1.920006 assigned positive charge : 309.1167 centred at (gu) : 87.70228 89.40612 89.58438 assigned negative charge : -307.1968 centred at (gu) : 87.88226 89.47723 89.59306 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6157 nv = 96 ne = 84 npr = 41754 no. pairs analyzed = 41754 no. exposed pairs = 2584 no. arc points = 18341 no. surface atoms = 879 nbur = 1176 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3371 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1722 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0564075E-09 3.0395904E-09 midg,1,midg; midg,igrid,midg 2.0276961E-08 -7.3278241E-09 1,midg,midg; igrid,midg,midg 6.0986387E-08 -1.7885288E-08 gauss-seidel spectral radius is 0.9882883 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 21:42:42 rms-change max change #iterations 0.1547890 25.41042 at 10iterations 1.6681649E-02 2.512649 at 20iterations 1.7903481E-03 0.2718658 at 30iterations 2.0288644E-04 3.0502319E-02 at 40iterations 2.5366677E-05 4.0464401E-03 at 50iterations finished qdiffx linear iterations at : 21:42:46 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 2.5366677E-05 4.0464401E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 21:42:46 4.163u 0.226s 0:04.65 94.1% 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 Sat Oct 8 2011 at 21:42:46 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2055 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 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: 2.000112 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): 5.451000 58.84800 ymin,ymax (A): 2.811000 49.81900 zmin,zma (A): 13.38600 55.87300 x,y,z range (A): 53.39700 47.00800 42.48700 scale (grids/A): 2.000112 object centre (A): 32.14950 26.31500 34.62950 number of atom coordinates read : 2055 total number of charged atoms : 1915 net assigned charge : 1.920006 assigned positive charge : 309.1167 centred at (gu) : 83.10651 88.21812 88.75301 assigned negative charge : -307.1968 centred at (gu) : 83.64686 88.43155 88.77914 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18341 grid for indexing accessible points = 1.400000 m= 24019 mr = 45375 m= 4021 mr = 17441 m= 296 mr = 2444 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.5200000 number of dielectric boundary points 28945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15137 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) : 0.6667041 object centre at (A) : 32.14950 26.31500 34.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0512101E-02 3.1803935E-03 midg,1,midg; midg,igrid,midg 4.0034395E-02 1.1069737E-03 1,midg,midg; igrid,midg,midg -3.4414738E-02 -4.5176800E-02 gauss-seidel spectral radius is 0.9987004 estimated iterations to convergence 220 setup time was (sec) 0.8400000 now iterating at: 21:42:47 rms-change max change #iterations 4.134346 226.0776 at 10iterations 1.969573 69.24336 at 20iterations 0.9339852 30.75864 at 30iterations 0.4463210 14.84326 at 40iterations 0.2136768 7.603345 at 50iterations 0.1022099 3.217819 at 60iterations 4.8454154E-02 1.693293 at 70iterations 2.3070890E-02 0.8062859 at 80iterations 1.1026029E-02 0.3547516 at 90iterations 5.2734576E-03 0.1906590 at 100iterations 2.5236635E-03 7.9963684E-02 at 110iterations 1.2031270E-03 4.1679382E-02 at 120iterations finished qdiffx linear iterations at : 21:42:56 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.2031270E-03 4.1679382E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 21:42:56 9.424u 0.254s 0:09.94 97.2% 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 21:42:56 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2055 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.000168 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): 5.451000 58.84800 ymin,ymax (A): 2.811000 49.81900 zmin,zma (A): 13.38600 55.87300 x,y,z range (A): 53.39700 47.00800 42.48700 scale (grids/A): 3.000168 object centre (A): 32.14950 26.31500 34.62950 number of atom coordinates read : 2055 total number of charged atoms : 1915 net assigned charge : 1.920006 assigned positive charge : 309.1167 centred at (gu) : 79.65961 87.32715 88.12936 assigned negative charge : -307.1968 centred at (gu) : 80.47021 87.64722 88.16859 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 152208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18341 grid for indexing accessible points = 1.400000 m= 76755 mr = 109816 m= 28495 mr = 62343 m= 7519 mr = 22688 m= 1242 mr = 5466 m= 68 mr = 795 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 573 time to turn everything in is 1.310000 number of dielectric boundary points 65166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15320 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) : 2.000112 object centre at (A) : 32.14950 26.31500 34.62950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1122247 5.5312505E-03 midg,1,midg; midg,igrid,midg 0.3357405 -7.6595522E-02 1,midg,midg; igrid,midg,midg -0.6052856 -0.6345972 gauss-seidel spectral radius is 0.9992669 estimated iterations to convergence 291 setup time was (sec) 1.660000 now iterating at: 21:42:58 rms-change max change #iterations 9.529507 374.8727 at 10iterations 5.611010 126.0804 at 20iterations 3.272673 68.19073 at 30iterations 1.907392 39.54357 at 40iterations 1.109132 21.02170 at 50iterations 0.6437445 13.75793 at 60iterations 0.3731398 8.063160 at 70iterations 0.2161678 4.805809 at 80iterations 0.1251157 2.392988 at 90iterations 7.2108760E-02 1.327293 at 100iterations 4.1701198E-02 0.7661815 at 110iterations 2.4082972E-02 0.4392153 at 120iterations 1.3912627E-02 0.2595544 at 130iterations 8.0235563E-03 0.1504760 at 140iterations 4.6415385E-03 9.1195107E-02 at 150iterations 2.6785552E-03 5.2076817E-02 at 160iterations 1.5520906E-03 3.6115646E-02 at 170iterations 8.9955539E-04 1.6189575E-02 at 180iterations finished qdiffx linear iterations at : 21:43:11 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 8.9955539E-04 1.6189575E-02 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.20000 DelPhi exited at 21:43:12 15.205u 0.270s 0:15.74 98.2% 0+0k 0+0io 0pf+0w