Mon Oct 10 11:05:27 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 Mon Oct 10 2011 at 11:05:27 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: SEP 550 has a net charge of -0.4750 !!! WARNING: HIR 737 has a net charge of 0.5140 !!! WARNING: HIT 846 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5046854 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 0.5046854 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 12.55303 assigned positive charge : 848.4094 centred at (gu) : 88.53685 90.68672 91.00883 assigned negative charge : -835.8640 centred at (gu) : 88.57233 90.63316 91.07497 start vw surface at 0.2300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8711 nv = 96 ne = 84 npr = 105298 no. pairs analyzed = 105298 no. exposed pairs = 6620 no. arc points = 44722 no. surface atoms = 2211 nbur = 3138 mkacc time = 0.2200000 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 = 1.680000 m= 325 mr = 4762 m= 0 mr = 9 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.4900000 number of dielectric boundary points 4265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4410 ## 695 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2135392E-10 -2.9672032E-11 midg,1,midg; midg,igrid,midg 8.3915028E-12 3.1170094E-10 1,midg,midg; igrid,midg,midg 3.2141836E-10 3.6581051E-11 gauss-seidel spectral radius is 0.9799606 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 11:05:28 rms-change max change #iterations 6.8808272E-02 10.16392 at 10iterations 3.8428167E-03 0.5726776 at 20iterations 4.1099408E-04 6.9566727E-02 at 30iterations 1.6982234E-04 2.8144360E-02 at 40iterations 8.6898479E-05 1.4198780E-02 at 50iterations finished qdiffx linear iterations at : 11:05:30 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 8.6898479E-05 1.4198780E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 11:05:31 3.554u 0.192s 0:04.10 91.2% 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 Mon Oct 10 2011 at 11:05:31 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: SEP 550 has a net charge of -0.4750 !!! WARNING: HIR 737 has a net charge of 0.5140 !!! WARNING: HIT 846 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.514056 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 1.514056 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 12.55303 assigned positive charge : 848.4094 centred at (gu) : 85.60883 92.05853 93.02498 assigned negative charge : -835.8640 centred at (gu) : 85.71712 91.89941 93.22501 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 99731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29305 mr = 70569 m= 2372 mr = 19912 m= 38 mr = 960 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1918 time to turn everything in is 0.7200000 number of dielectric boundary points 40005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 675 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 38794 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) : 0.5046854 object centre at (A) : 35.00350 -5.652501 2.905000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7600091E-03 5.3678697E-04 midg,1,midg; midg,igrid,midg -4.0173260E-03 1.8333271E-02 1,midg,midg; igrid,midg,midg 2.5442094E-02 -1.6572861E-02 gauss-seidel spectral radius is 0.9981055 estimated iterations to convergence 183 setup time was (sec) 1.010000 now iterating at: 11:05:32 rms-change max change #iterations 4.032810 152.1967 at 10iterations 1.655267 51.67845 at 20iterations 0.6767207 20.91129 at 30iterations 0.2773562 8.203793 at 40iterations 0.1138366 3.459440 at 50iterations 4.6667252E-02 1.499837 at 60iterations 1.9147305E-02 0.6000900 at 70iterations 7.8908363E-03 0.2472534 at 80iterations 3.2648537E-03 0.1117058 at 90iterations 1.3944446E-03 4.1548729E-02 at 100iterations 6.3539710E-04 2.2448540E-02 at 110iterations 3.4361603E-04 1.3719559E-02 at 120iterations finished qdiffx linear iterations at : 11:05:38 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 3.4361603E-04 1.3719559E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 11:05:39 7.150u 0.215s 0:07.67 95.9% 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 Mon Oct 10 2011 at 11:05:39 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: SEP 550 has a net charge of -0.4750 !!! WARNING: HIR 737 has a net charge of 0.5140 !!! WARNING: HIT 846 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.271084 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 2.271084 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 12.55303 assigned positive charge : 848.4094 centred at (gu) : 83.41276 93.08747 94.53694 assigned negative charge : -835.8640 centred at (gu) : 83.57586 92.84921 94.83769 start vw surface at 0.2100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 233207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 105878 mr = 173373 m= 26108 mr = 83902 m= 3393 mr = 18953 m= 151 mr = 2067 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 6314 time to turn everything in is 1.580000 number of dielectric boundary points 90413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 41405 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) : 1.514056 object centre at (A) : 35.00350 -5.652501 2.905000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7979602E-02 -6.1655279E-02 midg,1,midg; midg,igrid,midg -0.1713787 0.3920108 1,midg,midg; igrid,midg,midg 0.2554050 -0.5396191 gauss-seidel spectral radius is 0.9991639 estimated iterations to convergence 273 setup time was (sec) 1.860000 now iterating at: 11:05:41 rms-change max change #iterations 11.01831 297.4889 at 10iterations 6.339718 154.0160 at 20iterations 3.601490 81.49365 at 30iterations 2.037812 53.39635 at 40iterations 1.147934 27.35152 at 50iterations 0.6443304 13.52954 at 60iterations 0.3604999 6.827576 at 70iterations 0.2015411 3.841592 at 80iterations 0.1125297 2.278157 at 90iterations 6.2712356E-02 1.182351 at 100iterations 3.4923073E-02 0.6624455 at 110iterations 1.9450845E-02 0.3473563 at 120iterations 1.0816029E-02 0.2290039 at 130iterations 6.0240217E-03 0.1099167 at 140iterations 3.3569916E-03 5.9537649E-02 at 150iterations 1.8786422E-03 3.7487030E-02 at 160iterations 1.0613834E-03 1.8934250E-02 at 170iterations 6.0821889E-04 1.1557579E-02 at 180iterations finished qdiffx linear iterations at : 11:05:50 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 6.0821889E-04 1.1557579E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 11:05:51 11.580u 0.174s 0:12.07 97.3% 0+0k 0+0io 0pf+0w