Tue Oct 11 05:51:15 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 05:51:15 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 = 2048 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: 0.7216411 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): -4.703000 44.62900 ymin,ymax (A): -25.06500 22.10800 zmin,zma (A): 55.36600 98.09700 x,y,z range (A): 49.33200 47.17300 42.73100 scale (grids/A): 0.7216411 object centre (A): 19.96300 -1.478500 76.73150 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 91.10148 91.00004 90.20281 assigned negative charge : -302.6992 centred at (gu) : 90.98891 90.88310 90.26490 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7347 nv = 96 ne = 84 npr = 40920 no. pairs analyzed = 40920 no. exposed pairs = 2465 no. arc points = 17047 no. surface atoms = 843 nbur = 1205 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 515 mr = 4258 m= 5 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1481 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2181506E-07 4.7011920E-08 midg,1,midg; midg,igrid,midg 8.1929086E-09 1.9580489E-07 1,midg,midg; igrid,midg,midg 1.0476138E-08 1.9619036E-07 gauss-seidel spectral radius is 0.9899848 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 05:51:16 rms-change max change #iterations 0.2152149 35.31127 at 10iterations 2.7633792E-02 3.546156 at 20iterations 3.6857896E-03 0.5085773 at 30iterations 5.7791412E-04 7.4745178E-02 at 40iterations 1.2462703E-04 1.6020775E-02 at 50iterations finished qdiffx linear iterations at : 05:51:19 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.2462703E-04 1.6020775E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 05:51:19 3.416u 0.165s 0:04.07 87.7% 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 Tue Oct 11 2011 at 05:51:20 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 = 2048 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: 2.164923 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): -4.703000 44.62900 ymin,ymax (A): -25.06500 22.10800 zmin,zma (A): 55.36600 98.09700 x,y,z range (A): 49.33200 47.17300 42.73100 scale (grids/A): 2.164923 object centre (A): 19.96300 -1.478500 76.73150 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 93.30485 93.00015 90.60836 assigned negative charge : -302.6992 centred at (gu) : 92.96662 92.64938 90.79481 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17047 grid for indexing accessible points = 1.400000 m= 32388 mr = 55076 m= 6658 mr = 24908 m= 650 mr = 4458 m= 23 mr = 344 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 32296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15262 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) : 0.7216411 object centre at (A) : 19.96300 -1.478500 76.73150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2528009E-02 2.0969596E-02 midg,1,midg; midg,igrid,midg -3.5913032E-02 4.0565591E-02 1,midg,midg; igrid,midg,midg 6.4761169E-02 0.1104613 gauss-seidel spectral radius is 0.9988689 estimated iterations to convergence 235 setup time was (sec) 0.6300000 now iterating at: 05:51:20 rms-change max change #iterations 4.661165 195.8018 at 10iterations 2.333485 79.67036 at 20iterations 1.174147 38.00790 at 30iterations 0.5881314 17.15693 at 40iterations 0.2954898 8.609222 at 50iterations 0.1485703 4.572937 at 60iterations 7.4678883E-02 2.343304 at 70iterations 3.7609454E-02 1.090908 at 80iterations 1.8914293E-02 0.5282898 at 90iterations 9.5802750E-03 0.2650266 at 100iterations 4.8521264E-03 0.1753769 at 110iterations 2.4935829E-03 7.2525978E-02 at 120iterations finished qdiffx linear iterations at : 05:51:28 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.4935829E-03 7.2525978E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 05:51:28 7.954u 0.194s 0:08.59 94.7% 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 Tue Oct 11 2011 at 05:51:28 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 = 2048 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: 3.247385 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): -4.703000 44.62900 ymin,ymax (A): -25.06500 22.10800 zmin,zma (A): 55.36600 98.09700 x,y,z range (A): 49.33200 47.17300 42.73100 scale (grids/A): 3.247385 object centre (A): 19.96300 -1.478500 76.73150 number of atom coordinates read : 2048 total number of charged atoms : 1920 net assigned charge : 7.500009 assigned positive charge : 310.1990 centred at (gu) : 94.95725 94.50011 90.91259 assigned negative charge : -302.6992 centred at (gu) : 94.44987 93.97426 91.19234 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 178191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17047 grid for indexing accessible points = 1.400000 m= 99202 mr = 132571 m= 42550 mr = 83064 m= 12635 mr = 35219 m= 2654 mr = 9831 m= 378 mr = 1949 m= 29 mr = 263 m= 0 mr = 8 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 72734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15360 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) : 2.164923 object centre at (A) : 19.96300 -1.478500 76.73150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1065618 0.1475935 midg,1,midg; midg,igrid,midg -0.4021583 0.3186838 1,midg,midg; igrid,midg,midg 0.5364321 0.8315489 gauss-seidel spectral radius is 0.9993070 estimated iterations to convergence 300 setup time was (sec) 1.460000 now iterating at: 05:51:30 rms-change max change #iterations 10.35375 466.0243 at 10iterations 6.158522 152.5343 at 20iterations 3.657029 74.69460 at 30iterations 2.173635 39.78658 at 40iterations 1.289530 23.90985 at 50iterations 0.7591160 13.94217 at 60iterations 0.4475783 8.259346 at 70iterations 0.2638117 4.952821 at 80iterations 0.1555282 2.597118 at 90iterations 9.1678016E-02 1.459106 at 100iterations 5.4075997E-02 1.018534 at 110iterations 3.2009691E-02 0.5353279 at 120iterations 1.9036364E-02 0.3830357 at 130iterations 1.1492992E-02 0.2004681 at 140iterations 7.0917960E-03 0.1266708 at 150iterations 4.5213709E-03 8.3870411E-02 at 160iterations 3.0397575E-03 5.3581238E-02 at 170iterations 2.1719562E-03 3.9062500E-02 at 180iterations finished qdiffx linear iterations at : 05:51:41 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 2.1719562E-03 3.9062500E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 05:51:42 12.925u 0.242s 0:14.17 92.8% 0+0k 0+0io 0pf+0w