Tue Oct 11 06:27:23 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 06:27:23 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 = 2052 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: 0.6969596 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 0.6969596 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 89.08351 90.19431 91.12498 assigned negative charge : -309.0062 centred at (gu) : 89.03828 90.32777 91.18218 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6797 nv = 96 ne = 84 npr = 40654 no. pairs analyzed = 40654 no. exposed pairs = 2502 no. arc points = 17221 no. surface atoms = 858 nbur = 1194 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3860 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1654 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2385708E-08 2.5710333E-08 midg,1,midg; midg,igrid,midg 9.0420080E-08 -9.4172004E-09 1,midg,midg; igrid,midg,midg 3.0377876E-08 5.0731881E-08 gauss-seidel spectral radius is 0.9892683 estimated iterations to convergence 79 setup time was (sec) 0.4600000 now iterating at: 06:27:24 rms-change max change #iterations 0.1850425 26.02720 at 10iterations 2.2020862E-02 3.341160 at 20iterations 2.8412698E-03 0.3540239 at 30iterations 4.4829687E-04 5.4189682E-02 at 40iterations 9.8481374E-05 1.1974335E-02 at 50iterations finished qdiffx linear iterations at : 06:27:26 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 9.8481374E-05 1.1974335E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 06:27:28 3.034u 0.153s 0:04.85 65.5% 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 06:27:28 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 = 2052 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: 2.090879 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 2.090879 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 87.25059 90.58313 93.37490 assigned negative charge : -309.0062 centred at (gu) : 87.11510 90.98348 93.54675 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17221 grid for indexing accessible points = 1.400000 m= 28171 mr = 50696 m= 5292 mr = 21169 m= 428 mr = 3440 m= 20 mr = 192 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 539 time to turn everything in is 0.5200000 number of dielectric boundary points 30202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15429 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) : 0.6969596 object centre at (A) : -6.868000 42.67150 7.778501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1576894E-02 4.6582125E-02 midg,1,midg; midg,igrid,midg 3.6159243E-02 8.9206183E-03 1,midg,midg; igrid,midg,midg 2.1938561E-02 1.2162161E-02 gauss-seidel spectral radius is 0.9987972 estimated iterations to convergence 228 setup time was (sec) 0.8100000 now iterating at: 06:27:29 rms-change max change #iterations 4.473572 218.9428 at 10iterations 2.196094 80.27566 at 20iterations 1.081994 37.31440 at 30iterations 0.5331720 16.97623 at 40iterations 0.2620070 8.326545 at 50iterations 0.1291337 4.069489 at 60iterations 6.3433267E-02 1.902327 at 70iterations 3.1139575E-02 1.005882 at 80iterations 1.5417169E-02 0.4891729 at 90iterations 7.6063005E-03 0.2296295 at 100iterations 3.7587429E-03 0.1191864 at 110iterations 1.8790684E-03 6.2030792E-02 at 120iterations finished qdiffx linear iterations at : 06:27:35 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 1.8790684E-03 6.2030792E-02 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 06:27:36 7.404u 0.228s 0:07.92 96.2% 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 06:27:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.136318 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 3.136318 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 315.5060 centred at (gu) : 85.87589 90.87479 95.06228 assigned negative charge : -309.0062 centred at (gu) : 85.67265 91.47527 95.32008 start vw surface at 0.1600000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 165216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17221 grid for indexing accessible points = 1.400000 m= 88905 mr = 122239 m= 34924 mr = 73455 m= 9832 mr = 28359 m= 1928 mr = 7594 m= 224 mr = 1383 m= 12 mr = 131 m= 0 mr = 1 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1680 time to turn everything in is 1.680000 number of dielectric boundary points 67879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 15552 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) : 2.090879 object centre at (A) : -6.868000 42.67150 7.778501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4040669 0.3682115 midg,1,midg; midg,igrid,midg 0.2814695 9.1492914E-02 1,midg,midg; igrid,midg,midg 0.2935846 7.9212949E-02 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.990000 now iterating at: 06:27:38 rms-change max change #iterations 10.07952 331.1814 at 10iterations 5.951001 130.1468 at 20iterations 3.513755 74.17493 at 30iterations 2.064239 51.58164 at 40iterations 1.212450 25.03837 at 50iterations 0.7107901 14.63460 at 60iterations 0.4149003 7.598644 at 70iterations 0.2422854 4.736252 at 80iterations 0.1414748 2.977308 at 90iterations 8.2655430E-02 1.726622 at 100iterations 4.8390061E-02 0.9412394 at 110iterations 2.8254503E-02 0.5114937 at 120iterations 1.6532484E-02 0.2812523 at 130iterations 9.7013330E-03 0.1636786 at 140iterations 5.7298760E-03 0.1055756 at 150iterations 3.4127198E-03 6.5254211E-02 at 160iterations 2.0912618E-03 4.2838812E-02 at 170iterations 1.3231101E-03 2.5924683E-02 at 180iterations finished qdiffx linear iterations at : 06:27:50 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.3231101E-03 2.5924683E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 06:27:50 13.619u 0.237s 0:14.17 97.6% 0+0k 0+0io 0pf+0w