Mon Oct 10 11:12:21 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 11:12:21 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7461592 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 0.7461592 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 89.14348 89.67701 90.23265 assigned negative charge : -324.9440 centred at (gu) : 89.21771 89.70906 90.45009 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 43681 no. pairs analyzed = 43681 no. exposed pairs = 2723 no. arc points = 19449 no. surface atoms = 921 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 583 mr = 4498 m= 7 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.2800000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4156134E-07 -3.7584238E-07 midg,1,midg; midg,igrid,midg -6.6799792E-08 -1.3018614E-07 1,midg,midg; igrid,midg,midg -1.5791132E-08 -1.6052346E-07 gauss-seidel spectral radius is 0.9906431 estimated iterations to convergence 84 setup time was (sec) 0.5700000 now iterating at: 11:12:22 rms-change max change #iterations 0.2527221 34.39189 at 10iterations 3.3995561E-02 3.930365 at 20iterations 4.6728547E-03 0.5423698 at 30iterations 6.4718054E-04 7.6932907E-02 at 40iterations 8.8369830E-05 1.1016846E-02 at 50iterations finished qdiffx linear iterations at : 11:12:26 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 8.8369830E-05 1.1016846E-02 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 11:12:27 5.225u 0.455s 0:05.94 95.4% 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 11:12:27 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 2.238477 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 2.238477 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 87.43034 89.03103 90.69799 assigned negative charge : -324.9440 centred at (gu) : 87.65329 89.12720 91.35033 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19449 grid for indexing accessible points = 1.400000 m= 33993 mr = 58853 m= 7136 mr = 25697 m= 732 mr = 4854 m= 19 mr = 371 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2153 time to turn everything in is 0.7400000 number of dielectric boundary points 38029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15853 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) : 0.7461592 object centre at (A) : 1.320000 15.33150 20.28950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3441454E-03 -0.1477360 midg,1,midg; midg,igrid,midg -3.1353880E-02 -1.9247735E-02 1,midg,midg; igrid,midg,midg 1.2442400E-03 -3.5185737E-03 gauss-seidel spectral radius is 0.9989441 estimated iterations to convergence 243 setup time was (sec) 1.100000 now iterating at: 11:12:28 rms-change max change #iterations 5.207751 202.1116 at 10iterations 2.657100 97.06176 at 20iterations 1.360774 37.66367 at 30iterations 0.6978208 21.50758 at 40iterations 0.3569931 9.955196 at 50iterations 0.1828187 4.960230 at 60iterations 9.3430825E-02 2.576609 at 70iterations 4.7867216E-02 1.401761 at 80iterations 2.4532853E-02 0.7127600 at 90iterations 1.2602079E-02 0.3417616 at 100iterations 6.4680851E-03 0.1865921 at 110iterations 3.3198753E-03 8.9107513E-02 at 120iterations finished qdiffx linear iterations at : 11:12:40 total time elapsed so far: 12.85000 # loops : 120 mean,max change (kT/e) : 3.3198753E-03 8.9107513E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 11:12:40 13.014u 0.512s 0:13.88 97.4% 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 11:12:40 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 3.357716 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): -21.60100 24.24100 ymin,ymax (A): -7.954000 38.61700 zmin,zma (A): -3.566000 44.14500 x,y,z range (A): 45.84200 46.57100 47.71100 scale (grids/A): 3.357716 object centre (A): 1.320000 15.33150 20.28950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.9439 centred at (gu) : 86.14555 88.54646 91.04699 assigned negative charge : -324.9440 centred at (gu) : 86.47999 88.69084 92.02551 start vw surface at 0.1000000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 197737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19449 grid for indexing accessible points = 1.400000 m= 104996 mr = 142036 m= 44496 mr = 86821 m= 13609 mr = 36641 m= 2880 mr = 10580 m= 375 mr = 2066 m= 17 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 6999 time to turn everything in is 2.320000 number of dielectric boundary points 85724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.550000 number of grid points assigned charge 15912 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) : 2.238477 object centre at (A) : 1.320000 15.33150 20.28950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9672366E-02 -1.300679 midg,1,midg; midg,igrid,midg -0.3033265 -0.1096508 1,midg,midg; igrid,midg,midg 3.6605358E-02 -0.1365306 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.800000 now iterating at: 11:12:44 rms-change max change #iterations 11.18887 426.2174 at 10iterations 6.604057 122.7537 at 20iterations 3.903650 67.10492 at 30iterations 2.298646 42.64517 at 40iterations 1.359002 21.63217 at 50iterations 0.8007596 12.70985 at 60iterations 0.4708008 7.847684 at 70iterations 0.2776243 4.946074 at 80iterations 0.1632911 2.553413 at 90iterations 9.6209131E-02 1.605516 at 100iterations 5.6559030E-02 0.9416065 at 110iterations 3.3365529E-02 0.4967804 at 120iterations 1.9631647E-02 0.3201504 at 130iterations 1.1521210E-02 0.1851110 at 140iterations 6.7985142E-03 0.1032753 at 150iterations 4.0063420E-03 6.1282158E-02 at 160iterations 2.3605735E-03 3.9221764E-02 at 170iterations 1.3882504E-03 2.3933411E-02 at 180iterations finished qdiffx linear iterations at : 11:13:04 total time elapsed so far: 23.05000 # loops : 180 mean,max change (kT/e) : 1.3882504E-03 2.3933411E-02 energy calculations done at 23.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.22000 DelPhi exited at 11:13:05 23.224u 0.550s 0:24.13 98.5% 0+0k 0+0io 0pf+0w