Tue Oct 11 03:25:35 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 Tue Oct 11 2011 at 03:25:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7481349 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 0.7481349 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 176.9231 centred at (gu) : 89.31224 89.16929 88.31260 assigned negative charge : -171.4232 centred at (gu) : 89.01561 89.14897 88.33251 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4431 nv = 96 ne = 84 npr = 22628 no. pairs analyzed = 22628 no. exposed pairs = 1486 no. arc points = 11029 no. surface atoms = 501 nbur = 667 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 2287 m= 0 mr = 54 time to grow re-entrant surface = 3.0000001E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1100000 number of dielectric boundary points 2378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 888 ## 84 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7567267E-07 7.7315271E-08 midg,1,midg; midg,igrid,midg 1.2015649E-07 1.1172473E-07 1,midg,midg; igrid,midg,midg -9.0301604E-08 2.6494601E-07 gauss-seidel spectral radius is 0.9905909 estimated iterations to convergence 84 setup time was (sec) 0.2900000 now iterating at: 03:25:35 rms-change max change #iterations 0.1885465 37.63667 at 10iterations 2.5960287E-02 3.898912 at 20iterations 3.4988804E-03 0.6831989 at 30iterations 4.7280299E-04 9.0171814E-02 at 40iterations 6.3478539E-05 1.1566162E-02 at 50iterations finished qdiffx linear iterations at : 03:25:38 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 6.3478539E-05 1.1566162E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 03:25:39 3.237u 0.174s 0:03.96 85.8% 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 03:25:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.244405 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 2.244405 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 176.9231 centred at (gu) : 87.93690 87.50802 84.93805 assigned negative charge : -171.4232 centred at (gu) : 87.04699 87.44698 84.99767 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 46107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11029 grid for indexing accessible points = 1.400000 m= 17640 mr = 30027 m= 3576 mr = 13317 m= 354 mr = 2448 m= 15 mr = 208 m= 0 mr = 8 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.2400000 number of dielectric boundary points 21684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8471 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) : 0.7481349 object centre at (A) : 11.73450 20.63800 22.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9901197E-02 9.8557649E-03 midg,1,midg; midg,igrid,midg 4.3639008E-02 3.4420408E-02 1,midg,midg; igrid,midg,midg -2.9035116E-02 4.3874208E-02 gauss-seidel spectral radius is 0.9988537 estimated iterations to convergence 234 setup time was (sec) 0.4400000 now iterating at: 03:25:40 rms-change max change #iterations 3.713743 255.3001 at 10iterations 1.847363 77.18487 at 20iterations 0.9217446 37.08900 at 30iterations 0.4576861 18.05901 at 40iterations 0.2294680 8.121658 at 50iterations 0.1138400 4.202959 at 60iterations 5.6605246E-02 2.139094 at 70iterations 2.8274545E-02 1.015903 at 80iterations 1.4040196E-02 0.5389328 at 90iterations 6.9878730E-03 0.2610669 at 100iterations 3.4730446E-03 0.1302395 at 110iterations 1.7254913E-03 6.2751770E-02 at 120iterations finished qdiffx linear iterations at : 03:25:46 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.7254913E-03 6.2751770E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 03:25:47 7.465u 0.207s 0:08.39 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 Tue Oct 11 2011 at 03:25:47 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1168 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.366607 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): -6.973000 30.44200 ymin,ymax (A): 1.162000 40.11400 zmin,zma (A): -1.101000 46.48400 x,y,z range (A): 37.41500 38.95200 47.58500 scale (grids/A): 3.366607 object centre (A): 11.73450 20.63800 22.69150 number of atom coordinates read : 1168 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 176.9231 centred at (gu) : 86.90543 86.26202 82.40712 assigned negative charge : -171.4232 centred at (gu) : 85.57050 86.17056 82.49653 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 106156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11029 grid for indexing accessible points = 1.400000 m= 53885 mr = 72735 m= 22768 mr = 44086 m= 6773 mr = 18888 m= 1391 mr = 5299 m= 226 mr = 1127 m= 26 mr = 168 m= 0 mr = 21 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 432 time to turn everything in is 0.7400000 number of dielectric boundary points 48901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 8488 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) : 2.244405 object centre at (A) : 11.73450 20.63800 22.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3729264 7.7466674E-02 midg,1,midg; midg,igrid,midg 0.4027520 0.2943477 1,midg,midg; igrid,midg,midg -0.2342666 0.3085034 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 0.9600000 now iterating at: 03:25:48 rms-change max change #iterations 8.033146 378.1302 at 10iterations 4.675293 124.6264 at 20iterations 2.712314 61.70866 at 30iterations 1.575153 32.44217 at 40iterations 0.9165092 20.55609 at 50iterations 0.5307348 10.54771 at 60iterations 0.3077318 6.682058 at 70iterations 0.1788285 3.962285 at 80iterations 0.1037388 2.213097 at 90iterations 6.0300164E-02 1.324747 at 100iterations 3.4957040E-02 0.7596779 at 110iterations 2.0283369E-02 0.4401823 at 120iterations 1.1739467E-02 0.2563343 at 130iterations 6.8187802E-03 0.1430664 at 140iterations 3.9625741E-03 7.7949047E-02 at 150iterations 2.3049936E-03 5.1315308E-02 at 160iterations 1.3343989E-03 2.9338926E-02 at 170iterations 7.7615271E-04 1.6006470E-02 at 180iterations finished qdiffx linear iterations at : 03:25:59 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 7.7615271E-04 1.6006470E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 03:26:00 11.849u 0.204s 0:12.37 97.3% 0+0k 0+0io 0pf+0w