Wed Dec 28 11:01:17 PST 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 Wed Dec 28 2011 at 11:01:17 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 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: 0.6495638 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 0.6495638 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.000005 assigned positive charge : 289.7680 centred at (gu) : 89.88862 88.49342 89.99943 assigned negative charge : -287.7683 centred at (gu) : 90.00799 88.35651 90.08691 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5783 nv = 96 ne = 84 npr = 40947 no. pairs analyzed = 40947 no. exposed pairs = 2440 no. arc points = 17195 no. surface atoms = 837 nbur = 1141 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3253 m= 6 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1736 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3741993E-08 -5.7722302E-09 midg,1,midg; midg,igrid,midg -1.5951233E-08 1.3915280E-08 1,midg,midg; igrid,midg,midg 1.7631370E-08 -9.1814139E-09 gauss-seidel spectral radius is 0.9876638 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 11:01:18 rms-change max change #iterations 0.1322948 23.27006 at 10iterations 1.3350412E-02 2.026963 at 20iterations 1.3771558E-03 0.2442775 at 30iterations 1.4116862E-04 2.7191162E-02 at 40iterations 1.4175002E-05 1.9803047E-03 at 50iterations finished qdiffx linear iterations at : 11:01:23 total time elapsed so far: 4.920000 # loops : 50 mean,max change (kT/e) : 1.4175002E-05 1.9803047E-03 energy calculations done at 4.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 11:01:24 5.096u 0.317s 0:06.44 83.8% 0+0k 0+0io 6pf+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 Wed Dec 28 2011 at 11:01:24 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 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: 1.948691 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 1.948691 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.000005 assigned positive charge : 289.7680 centred at (gu) : 89.66571 85.48018 89.99823 assigned negative charge : -287.7683 centred at (gu) : 90.02419 85.06978 90.26097 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17195 grid for indexing accessible points = 1.400000 m= 23804 mr = 42121 m= 4200 mr = 18480 m= 283 mr = 2827 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.5800000 number of dielectric boundary points 25632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14555 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) : 0.6495638 object centre at (A) : 45.79950 18.90300 67.26801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6082437E-03 1.9959835E-02 midg,1,midg; midg,igrid,midg -1.2853736E-02 3.9953455E-02 1,midg,midg; igrid,midg,midg 1.1081477E-02 -5.1057735E-03 gauss-seidel spectral radius is 0.9986198 estimated iterations to convergence 213 setup time was (sec) 0.9600000 now iterating at: 11:01:25 rms-change max change #iterations 3.705223 177.3087 at 10iterations 1.732552 69.01145 at 20iterations 0.8062575 26.64456 at 30iterations 0.3776323 13.45532 at 40iterations 0.1758921 5.757484 at 50iterations 8.1962056E-02 2.822584 at 60iterations 3.8196478E-02 1.312637 at 70iterations 1.7818980E-02 0.6843629 at 80iterations 8.2812933E-03 0.3009644 at 90iterations 3.8537586E-03 0.1381750 at 100iterations 1.8025120E-03 6.1741829E-02 at 110iterations 8.4379542E-04 2.8247833E-02 at 120iterations finished qdiffx linear iterations at : 11:01:36 total time elapsed so far: 11.73000 # loops : 120 mean,max change (kT/e) : 8.4379542E-04 2.8247833E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 11:01:37 11.915u 0.478s 0:13.18 93.9% 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 Wed Dec 28 2011 at 11:01:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 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: 2.923037 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 2.923037 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.000005 assigned positive charge : 289.7680 centred at (gu) : 89.49863 83.22042 89.99726 assigned negative charge : -287.7683 centred at (gu) : 90.03642 82.60471 90.39147 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 140483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17195 grid for indexing accessible points = 1.400000 m= 74804 mr = 101741 m= 30183 mr = 62575 m= 7716 mr = 25416 m= 1227 mr = 6072 m= 97 mr = 891 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 1.480000 number of dielectric boundary points 57764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 14768 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) : 1.948691 object centre at (A) : 45.79950 18.90300 67.26801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6136142E-02 0.2030622 midg,1,midg; midg,igrid,midg -0.2051615 0.3774577 1,midg,midg; igrid,midg,midg 7.3532596E-02 -3.9455928E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 1.910000 now iterating at: 11:01:39 rms-change max change #iterations 8.685463 423.8320 at 10iterations 5.019483 139.7704 at 20iterations 2.879964 58.23235 at 30iterations 1.651822 34.52523 at 40iterations 0.9479102 20.44117 at 50iterations 0.5419499 10.70935 at 60iterations 0.3096120 6.774526 at 70iterations 0.1768852 3.553928 at 80iterations 0.1008314 2.333954 at 90iterations 5.7528164E-02 1.147984 at 100iterations 3.2847412E-02 0.6126308 at 110iterations 1.8733757E-02 0.3758707 at 120iterations 1.0669350E-02 0.2057018 at 130iterations 6.1125900E-03 0.1451335 at 140iterations 3.4803709E-03 7.6876640E-02 at 150iterations 1.9772875E-03 3.8200378E-02 at 160iterations 1.1273988E-03 2.1028519E-02 at 170iterations 6.4364774E-04 1.2332916E-02 at 180iterations finished qdiffx linear iterations at : 11:01:58 total time elapsed so far: 19.93000 # loops : 180 mean,max change (kT/e) : 6.4364774E-04 1.2332916E-02 energy calculations done at 19.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.11000 DelPhi exited at 11:01:58 20.113u 0.506s 0:21.28 96.8% 0+0k 0+0io 0pf+0w