Mon Oct 10 17:05:21 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 17:05:21 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5623924 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 0.5623924 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.02811 assigned positive charge : 642.4292 centred at (gu) : 91.01293 91.44348 88.91903 assigned negative charge : -594.4050 centred at (gu) : 90.96620 91.39827 88.98605 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8429 nv = 96 ne = 84 npr = 70863 no. pairs analyzed = 70863 no. exposed pairs = 6286 no. arc points = 46629 no. surface atoms = 2049 nbur = 1993 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 374 mr = 3311 m= 0 mr = 7 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 5485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4775 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10866 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5115337E-09 3.4646219E-09 midg,1,midg; midg,igrid,midg 3.4406142E-09 8.7879446E-09 1,midg,midg; igrid,midg,midg 3.7766870E-09 7.9623979E-09 gauss-seidel spectral radius is 0.9838037 estimated iterations to convergence 65 setup time was (sec) 0.7300000 now iterating at: 17:05:22 rms-change max change #iterations 9.9887297E-02 15.82100 at 10iterations 7.5946092E-03 1.146652 at 20iterations 9.6754119E-04 0.1148529 at 30iterations 2.4511496E-04 1.6223907E-02 at 40iterations 7.1292663E-05 4.2037964E-03 at 50iterations finished qdiffx linear iterations at : 17:05:25 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 7.1292663E-05 4.2037964E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 17:05:26 4.194u 0.249s 0:04.82 91.9% 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 Mon Oct 10 2011 at 17:05:26 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.687177 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 1.687177 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.02811 assigned positive charge : 642.4292 centred at (gu) : 93.03765 94.32894 86.75545 assigned negative charge : -594.4050 centred at (gu) : 92.89852 94.19463 86.95804 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 90078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46629 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24888 mr = 51267 m= 2582 mr = 14496 m= 104 mr = 972 m= 0 mr = 8 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 50909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 30124 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) : 0.5623924 object centre at (A) : -11.78300 44.74150 58.16450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0078445E-02 2.4532598E-02 midg,1,midg; midg,igrid,midg 3.5794180E-02 7.6699831E-02 1,midg,midg; igrid,midg,midg 4.4038486E-02 0.1066316 gauss-seidel spectral radius is 0.9984571 estimated iterations to convergence 202 setup time was (sec) 1.110000 now iterating at: 17:05:27 rms-change max change #iterations 4.287957 162.1763 at 10iterations 1.899706 61.31007 at 20iterations 0.8481230 26.43438 at 30iterations 0.3777211 12.71209 at 40iterations 0.1684690 5.700067 at 50iterations 7.5108126E-02 2.667848 at 60iterations 3.3489201E-02 1.113319 at 70iterations 1.4950412E-02 0.4852161 at 80iterations 6.7162234E-03 0.2183685 at 90iterations 3.0210849E-03 0.1040802 at 100iterations 1.3680687E-03 4.8179626E-02 at 110iterations 6.2272948E-04 2.1785736E-02 at 120iterations finished qdiffx linear iterations at : 17:05:36 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 6.2272948E-04 2.1785736E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 17:05:36 9.815u 0.272s 0:10.42 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 Mon Oct 10 2011 at 17:05:36 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4042 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.530766 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): -43.40700 19.84100 ymin,ymax (A): 14.21900 75.26400 zmin,zma (A): 26.51400 89.81499 x,y,z range (A): 63.24800 61.04500 63.30099 scale (grids/A): 2.530766 object centre (A): -11.78300 44.74150 58.16450 number of atom coordinates read : 4042 total number of charged atoms : 3914 net assigned charge : 48.02811 assigned positive charge : 642.4292 centred at (gu) : 94.55614 96.49327 85.13294 assigned negative charge : -594.4050 centred at (gu) : 94.34773 96.29198 85.43699 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 207981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46629 grid for indexing accessible points = 1.400000 m= 84573 mr = 127680 m= 23506 mr = 59967 m= 3809 mr = 15575 m= 289 mr = 2003 m= 6 mr = 94 m= 0 mr = 4 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 114841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 31296 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) : 1.687177 object centre at (A) : -11.78300 44.74150 58.16450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9998838 0.3757536 midg,1,midg; midg,igrid,midg 0.6003658 0.8651740 1,midg,midg; igrid,midg,midg 0.3358375 1.472639 gauss-seidel spectral radius is 0.9992903 estimated iterations to convergence 296 setup time was (sec) 2.260000 now iterating at: 17:05:39 rms-change max change #iterations 11.29683 307.2140 at 10iterations 6.875875 175.8856 at 20iterations 4.157562 108.4866 at 30iterations 2.494835 61.38424 at 40iterations 1.483737 31.33829 at 50iterations 0.8821279 19.91229 at 60iterations 0.5206822 12.33214 at 70iterations 0.3081970 6.739485 at 80iterations 0.1817434 3.618431 at 90iterations 0.1070038 2.260548 at 100iterations 6.2814802E-02 1.110891 at 110iterations 3.6794052E-02 0.8004298 at 120iterations 2.1572890E-02 0.3881540 at 130iterations 1.2626414E-02 0.2372055 at 140iterations 7.3766611E-03 0.1429691 at 150iterations 4.3228655E-03 8.1242561E-02 at 160iterations 2.5239259E-03 4.6401978E-02 at 170iterations 1.4721776E-03 2.5444031E-02 at 180iterations finished qdiffx linear iterations at : 17:05:53 total time elapsed so far: 16.72000 # loops : 180 mean,max change (kT/e) : 1.4721776E-03 2.5444031E-02 energy calculations done at 16.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 17:05:54 16.890u 0.322s 0:17.74 97.0% 0+0k 0+0io 0pf+0w