Tue Oct 11 06:47:11 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 06:47:12 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 = 2057 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: 0.7550051 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 0.7550051 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 89.41557 91.02810 89.67020 assigned negative charge : -303.7472 centred at (gu) : 89.53719 90.88649 89.60226 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8067 nv = 96 ne = 84 npr = 41192 no. pairs analyzed = 41192 no. exposed pairs = 2535 no. arc points = 17201 no. surface atoms = 864 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 645 mr = 4696 m= 6 mr = 109 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 0.2600000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1457 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5166683E-08 2.5148594E-07 midg,1,midg; midg,igrid,midg -4.3976147E-09 4.3585331E-07 1,midg,midg; igrid,midg,midg 3.7327885E-07 1.8228837E-08 gauss-seidel spectral radius is 0.9908447 estimated iterations to convergence 85 setup time was (sec) 0.5800000 now iterating at: 06:47:13 rms-change max change #iterations 0.2542005 31.04288 at 10iterations 3.5882432E-02 5.353104 at 20iterations 5.3611090E-03 0.7156024 at 30iterations 9.4276370E-04 0.1116180 at 40iterations 2.4199809E-04 2.6367188E-02 at 50iterations finished qdiffx linear iterations at : 06:47:17 total time elapsed so far: 5.120000 # loops : 50 mean,max change (kT/e) : 2.4199809E-04 2.6367188E-02 energy calculations done at 5.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 06:47:18 5.306u 0.475s 0:06.08 94.9% 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 Tue Oct 11 2011 at 06:47:18 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 = 2057 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: 2.265015 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 2.265015 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 88.24686 93.08411 89.01053 assigned negative charge : -303.7472 centred at (gu) : 88.61178 92.65970 88.80678 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17201 grid for indexing accessible points = 1.400000 m= 37037 mr = 60657 m= 8508 mr = 28614 m= 876 mr = 5879 m= 30 mr = 457 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 35780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 15373 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) : 0.7550051 object centre at (A) : 10.69300 62.41300 26.92200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7222517E-02 2.6322406E-02 midg,1,midg; midg,igrid,midg -5.1577818E-02 6.6426471E-02 1,midg,midg; igrid,midg,midg 0.1227572 5.2653547E-02 gauss-seidel spectral radius is 0.9989524 estimated iterations to convergence 244 setup time was (sec) 1.140000 now iterating at: 06:47:19 rms-change max change #iterations 5.083816 212.6177 at 10iterations 2.612562 85.34634 at 20iterations 1.344865 36.20371 at 30iterations 0.6944824 19.50568 at 40iterations 0.3567958 11.03266 at 50iterations 0.1842145 5.048721 at 60iterations 9.5116854E-02 2.578644 at 70iterations 4.9044043E-02 1.350456 at 80iterations 2.5451655E-02 0.6796188 at 90iterations 1.3280122E-02 0.3812580 at 100iterations 6.9519654E-03 0.1987858 at 110iterations 3.7135116E-03 0.1133575 at 120iterations finished qdiffx linear iterations at : 06:47:30 total time elapsed so far: 12.17000 # loops : 120 mean,max change (kT/e) : 3.7135116E-03 0.1133575 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 06:47:31 12.350u 0.501s 0:13.28 96.7% 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 06:47:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 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: 3.397523 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 3.397523 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 87.37013 94.62610 88.51588 assigned negative charge : -303.7472 centred at (gu) : 87.91770 93.98947 88.21017 start vw surface at 0.1000000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 195179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17201 grid for indexing accessible points = 1.400000 m= 111223 mr = 145611 m= 50312 mr = 93303 m= 16279 mr = 41716 m= 3555 mr = 12961 m= 504 mr = 2570 m= 38 mr = 303 m= 0 mr = 15 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.360000 number of dielectric boundary points 80611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 15432 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) : 2.265015 object centre at (A) : 10.69300 62.41300 26.92200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3733298 9.3075655E-02 midg,1,midg; midg,igrid,midg -0.5142244 0.6102975 1,midg,midg; igrid,midg,midg 0.8318454 0.3114850 gauss-seidel spectral radius is 0.9993309 estimated iterations to convergence 305 setup time was (sec) 2.730000 now iterating at: 06:47:34 rms-change max change #iterations 10.99743 255.2398 at 10iterations 6.655161 126.5003 at 20iterations 3.987356 83.42102 at 30iterations 2.387091 44.13398 at 40iterations 1.427101 25.11172 at 50iterations 0.8530889 16.71860 at 60iterations 0.5080267 8.940132 at 70iterations 0.3031616 5.053984 at 80iterations 0.1803346 3.157013 at 90iterations 0.1075090 1.898251 at 100iterations 6.3946791E-02 1.138449 at 110iterations 3.8248498E-02 0.6629360 at 120iterations 2.3046246E-02 0.3849144 at 130iterations 1.4096578E-02 0.2394919 at 140iterations 8.8744480E-03 0.1506500 at 150iterations 5.8488832E-03 0.1065664 at 160iterations 4.0718340E-03 6.9221497E-02 at 170iterations 3.0325053E-03 5.1376343E-02 at 180iterations finished qdiffx linear iterations at : 06:47:53 total time elapsed so far: 21.40000 # loops : 180 mean,max change (kT/e) : 3.0325053E-03 5.1376343E-02 energy calculations done at 21.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.56000 DelPhi exited at 06:47:54 21.566u 0.559s 0:22.56 98.0% 0+0k 0+0io 0pf+0w