Tue Oct 11 03:13:42 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 03:13:43 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 = 3411 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5393448 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 0.5393448 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3270 net assigned charge : -7.999979 assigned positive charge : 516.2803 centred at (gu) : 91.74094 87.90588 92.26184 assigned negative charge : -524.2817 centred at (gu) : 91.69579 87.89443 92.29906 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6352 nv = 96 ne = 84 npr = 69687 no. pairs analyzed = 69687 no. exposed pairs = 4233 no. arc points = 29879 no. surface atoms = 1410 nbur = 2001 mkacc time = 0.1200000 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 = 1.596000 m= 293 mr = 3344 m= 2 mr = 13 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 0.2500000 number of dielectric boundary points 3290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3043 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2126619E-11 -1.0556973E-09 midg,1,midg; midg,igrid,midg -7.4487327E-10 -1.8636556E-10 1,midg,midg; igrid,midg,midg -4.2224010E-10 -1.5328287E-10 gauss-seidel spectral radius is 0.9823126 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 03:13:43 rms-change max change #iterations 7.5658895E-02 12.77894 at 10iterations 5.2245925E-03 0.8203011 at 20iterations 5.4141547E-04 8.1962705E-02 at 30iterations 1.1894020E-04 1.5312672E-02 at 40iterations 3.1549826E-05 4.2057037E-03 at 50iterations finished qdiffx linear iterations at : 03:13:46 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.1549826E-05 4.2057037E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:13:47 3.495u 0.180s 0:04.28 85.7% 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 03:13:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.618035 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 1.618035 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3270 net assigned charge : -7.999979 assigned positive charge : 516.2803 centred at (gu) : 95.22181 83.71650 96.78441 assigned negative charge : -524.2817 centred at (gu) : 95.08682 83.68293 96.89642 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 71291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21690 mr = 48653 m= 2244 mr = 14798 m= 71 mr = 1061 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 684 time to turn everything in is 0.3600000 number of dielectric boundary points 30778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24923 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) : 0.5393448 object centre at (A) : -15.87300 -25.82400 -1.269001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4637792E-02 -1.4654282E-02 midg,1,midg; midg,igrid,midg -5.1741246E-03 -4.6858317E-03 1,midg,midg; igrid,midg,midg -5.5246153E-03 -4.6209716E-03 gauss-seidel spectral radius is 0.9981849 estimated iterations to convergence 186 setup time was (sec) 0.5700000 now iterating at: 03:13:48 rms-change max change #iterations 3.555953 160.9933 at 10iterations 1.481379 56.26608 at 20iterations 0.6189749 23.24040 at 30iterations 0.2573206 8.544189 at 40iterations 0.1077054 3.878108 at 50iterations 4.4730082E-02 1.691586 at 60iterations 1.8731069E-02 0.6114826 at 70iterations 7.8714984E-03 0.2745972 at 80iterations 3.3429584E-03 0.1118317 at 90iterations 1.4453136E-03 4.9320698E-02 at 100iterations 6.4973324E-04 2.2724152E-02 at 110iterations 3.0562820E-04 1.2819767E-02 at 120iterations finished qdiffx linear iterations at : 03:13:55 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0562820E-04 1.2819767E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 03:13:55 7.887u 0.209s 0:08.43 95.8% 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 03:13:55 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 = 3411 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.427052 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): -43.06200 11.31600 ymin,ymax (A): -55.27600 3.628000 zmin,zma (A): -34.27200 31.73400 x,y,z range (A): 54.37800 58.90400 66.00600 scale (grids/A): 2.427052 object centre (A): -15.87300 -25.82400 -1.269001 number of atom coordinates read : 3411 total number of charged atoms : 3270 net assigned charge : -7.999979 assigned positive charge : 516.2803 centred at (gu) : 97.83274 80.57432 100.1763 assigned negative charge : -524.2817 centred at (gu) : 97.62990 80.52433 100.3444 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 75629 mr = 119311 m= 20999 mr = 59806 m= 3539 mr = 15594 m= 239 mr = 2295 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2135 time to turn everything in is 0.8700000 number of dielectric boundary points 69386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 26134 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) : 1.618035 object centre at (A) : -15.87300 -25.82400 -1.269001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4740857 -0.3483609 midg,1,midg; midg,igrid,midg -2.7000489E-02 -8.5323416E-03 1,midg,midg; igrid,midg,midg -9.0681769E-02 -4.5127831E-02 gauss-seidel spectral radius is 0.9991445 estimated iterations to convergence 270 setup time was (sec) 1.100000 now iterating at: 03:13:57 rms-change max change #iterations 9.272417 255.0490 at 10iterations 5.233423 134.5189 at 20iterations 2.932894 68.79340 at 30iterations 1.641995 40.75873 at 40iterations 0.9129571 25.40645 at 50iterations 0.5071588 10.78983 at 60iterations 0.2809131 5.791650 at 70iterations 0.1555249 3.271734 at 80iterations 8.6202428E-02 1.774353 at 90iterations 4.7587488E-02 0.9822602 at 100iterations 2.6261175E-02 0.5580766 at 110iterations 1.4521503E-02 0.3331013 at 120iterations 8.0266157E-03 0.1644707 at 130iterations 4.4494472E-03 8.2676888E-02 at 140iterations 2.4741364E-03 5.2257538E-02 at 150iterations 1.3825716E-03 2.8137207E-02 at 160iterations 7.7788997E-04 1.4222622E-02 at 170iterations 4.4449349E-04 8.7718964E-03 at 180iterations finished qdiffx linear iterations at : 03:14:09 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 4.4449349E-04 8.7718964E-03 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 03:14:09 13.064u 0.219s 0:13.80 96.1% 0+0k 0+0io 0pf+0w