Sun Oct 9 11:15:09 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 Sun Oct 9 2011 at 11:15:09 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 = 2869 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5842866 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 0.5842866 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.500018 assigned positive charge : 431.5110 centred at (gu) : 90.56660 91.02064 88.97435 assigned negative charge : -425.0128 centred at (gu) : 90.56632 91.03307 89.05110 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6828 nv = 96 ne = 84 npr = 54055 no. pairs analyzed = 54055 no. exposed pairs = 4131 no. arc points = 29226 no. surface atoms = 1368 nbur = 1501 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 = 1.484000 m= 354 mr = 3372 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2891 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3993835E-09 -1.7903384E-10 midg,1,midg; midg,igrid,midg 1.5300238E-09 1.6637832E-09 1,midg,midg; igrid,midg,midg 1.4258188E-09 1.8549583E-09 gauss-seidel spectral radius is 0.9848883 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 11:15:10 rms-change max change #iterations 9.6424624E-02 16.22441 at 10iterations 7.7389623E-03 1.164379 at 20iterations 6.9911813E-04 9.2649460E-02 at 30iterations 1.0351735E-04 1.4610291E-02 at 40iterations 2.3495517E-05 3.1440258E-03 at 50iterations finished qdiffx linear iterations at : 11:15:13 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.3495517E-05 3.1440258E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 11:15:13 3.345u 0.216s 0:04.12 86.1% 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 Sun Oct 9 2011 at 11:15:13 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 = 2869 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.752860 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 1.752860 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.500018 assigned positive charge : 431.5110 centred at (gu) : 91.69882 93.06099 86.92201 assigned negative charge : -425.0128 centred at (gu) : 91.69891 93.09937 87.15325 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29226 grid for indexing accessible points = 1.400000 m= 24424 mr = 49031 m= 3350 mr = 16462 m= 129 mr = 1781 m= 0 mr = 13 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.5300000 number of dielectric boundary points 35135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21824 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) : 0.5842866 object centre at (A) : 10.58250 0.3665009 28.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2624084E-02 -5.0759269E-03 midg,1,midg; midg,igrid,midg 2.2841869E-02 2.8487368E-02 1,midg,midg; igrid,midg,midg -5.9097279E-03 1.6430782E-02 gauss-seidel spectral radius is 0.9984503 estimated iterations to convergence 202 setup time was (sec) 0.8400000 now iterating at: 11:15:14 rms-change max change #iterations 3.785710 179.0421 at 10iterations 1.675421 60.05225 at 20iterations 0.7445680 26.91985 at 30iterations 0.3315618 11.16857 at 40iterations 0.1475355 4.973209 at 50iterations 6.5791830E-02 2.099735 at 60iterations 2.9203951E-02 1.166290 at 70iterations 1.3023122E-02 0.4409447 at 80iterations 5.8016893E-03 0.2277415 at 90iterations 2.6020985E-03 9.5371246E-02 at 100iterations 1.1683239E-03 4.0561199E-02 at 110iterations 5.2801141E-04 1.6347885E-02 at 120iterations finished qdiffx linear iterations at : 11:15:22 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 5.2801141E-04 1.6347885E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 11:15:23 8.481u 0.220s 0:09.09 95.7% 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 Sun Oct 9 2011 at 11:15:23 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 = 2869 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.629290 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): -19.88200 41.04700 ymin,ymax (A): -29.14400 29.87700 zmin,zma (A): 1.352000 55.90200 x,y,z range (A): 60.92900 59.02100 54.55000 scale (grids/A): 2.629290 object centre (A): 10.58250 0.3665009 28.62700 number of atom coordinates read : 2869 total number of charged atoms : 2798 net assigned charge : 6.500018 assigned positive charge : 431.5110 centred at (gu) : 92.54811 94.59126 85.38284 assigned negative charge : -425.0128 centred at (gu) : 92.54830 94.64903 85.72990 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 172943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29226 grid for indexing accessible points = 1.400000 m= 80719 mr = 120656 m= 26627 mr = 62457 m= 5753 mr = 20025 m= 569 mr = 3937 m= 12 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 1.290000 number of dielectric boundary points 79250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 22373 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) : 1.752860 object centre at (A) : 10.58250 0.3665009 28.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1481761 -5.3322148E-02 midg,1,midg; midg,igrid,midg 0.2821012 0.4112555 1,midg,midg; igrid,midg,midg -0.1451199 0.3438121 gauss-seidel spectral radius is 0.9992274 estimated iterations to convergence 284 setup time was (sec) 1.620000 now iterating at: 11:15:24 rms-change max change #iterations 9.537179 308.3515 at 10iterations 5.605727 135.3821 at 20iterations 3.267796 74.81786 at 30iterations 1.888157 39.51337 at 40iterations 1.091758 25.12090 at 50iterations 0.6274727 12.62969 at 60iterations 0.3592137 7.082072 at 70iterations 0.2054919 4.477486 at 80iterations 0.1174392 2.274390 at 90iterations 6.7052335E-02 1.335365 at 100iterations 3.8131777E-02 0.7721004 at 110iterations 2.1684282E-02 0.4190693 at 120iterations 1.2355051E-02 0.2543583 at 130iterations 7.0355022E-03 0.1526548 at 140iterations 4.0137260E-03 7.9238892E-02 at 150iterations 2.2901890E-03 4.7088623E-02 at 160iterations 1.3065648E-03 2.6020050E-02 at 170iterations 7.4965321E-04 1.4793396E-02 at 180iterations finished qdiffx linear iterations at : 11:15:35 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 7.4965321E-04 1.4793396E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 11:15:36 12.464u 0.232s 0:13.05 97.2% 0+0k 0+0io 0pf+0w