Sun Oct 9 14:47:56 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 14:47:56 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 = 2505 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: 0.5631040 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 0.5631040 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000015 assigned positive charge : 375.9167 centred at (gu) : 90.76062 88.95934 86.82612 assigned negative charge : -369.9175 centred at (gu) : 90.50049 89.13990 86.91122 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5381 nv = 96 ne = 84 npr = 46549 no. pairs analyzed = 46549 no. exposed pairs = 3618 no. arc points = 26891 no. surface atoms = 1215 nbur = 1290 mkacc time = 9.9999994E-02 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 = 1.512000 m= 214 mr = 2319 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2723 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2358098E-09 -9.7957656E-11 midg,1,midg; midg,igrid,midg 3.1282317E-09 -9.5354546E-10 1,midg,midg; igrid,midg,midg -1.7305555E-09 3.8442405E-09 gauss-seidel spectral radius is 0.9837124 estimated iterations to convergence 64 setup time was (sec) 0.4900000 now iterating at: 14:47:57 rms-change max change #iterations 7.4294135E-02 14.14400 at 10iterations 5.3635011E-03 0.8952637 at 20iterations 4.8228056E-04 0.1155472 at 30iterations 7.0700487E-05 1.8527985E-02 at 40iterations 1.4436754E-05 3.7689209E-03 at 50iterations finished qdiffx linear iterations at : 14:47:59 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.4436754E-05 3.7689209E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:48:00 3.082u 0.151s 0:03.54 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 Sun Oct 9 2011 at 14:48:00 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 = 2505 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: 1.689312 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 1.689312 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000015 assigned positive charge : 375.9167 centred at (gu) : 92.28106 86.87751 80.47767 assigned negative charge : -369.9175 centred at (gu) : 91.50117 87.41930 80.73351 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26891 grid for indexing accessible points = 1.400000 m= 16795 mr = 35401 m= 1764 mr = 10731 m= 79 mr = 789 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 30100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18224 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) : 0.5631040 object centre at (A) : 7.800500 3.826501 21.44450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8857121E-02 3.7361900E-04 midg,1,midg; midg,igrid,midg 2.0309824E-02 -8.4230397E-03 1,midg,midg; igrid,midg,midg -2.9064247E-02 2.3043673E-02 gauss-seidel spectral radius is 0.9982772 estimated iterations to convergence 191 setup time was (sec) 0.6700000 now iterating at: 14:48:01 rms-change max change #iterations 3.212017 173.2203 at 10iterations 1.357394 56.43934 at 20iterations 0.5741684 24.12327 at 30iterations 0.2430344 10.34412 at 40iterations 0.1031509 4.069216 at 50iterations 4.3713477E-02 1.701603 at 60iterations 1.8596876E-02 0.6787252 at 70iterations 7.8939022E-03 0.2900209 at 80iterations 3.3798681E-03 0.1181259 at 90iterations 1.4503478E-03 5.5534363E-02 at 100iterations 6.2450004E-04 2.6245117E-02 at 110iterations 2.7160914E-04 1.0803223E-02 at 120iterations finished qdiffx linear iterations at : 14:48:07 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 2.7160914E-04 1.0803223E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 14:48:07 6.878u 0.157s 0:07.34 95.6% 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 14:48:07 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 = 2505 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: 2.533968 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): -20.77300 36.37400 ymin,ymax (A): -22.07500 29.72800 zmin,zma (A): -10.16600 53.05500 x,y,z range (A): 57.14700 51.80300 63.22100 scale (grids/A): 2.533968 object centre (A): 7.800500 3.826501 21.44450 number of atom coordinates read : 2505 total number of charged atoms : 2364 net assigned charge : 6.000015 assigned positive charge : 375.9167 centred at (gu) : 93.42149 85.31607 75.71645 assigned negative charge : -369.9175 centred at (gu) : 92.25172 86.12890 76.10022 start vw surface at 0.1500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 135067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26891 grid for indexing accessible points = 1.400000 m= 57584 mr = 87448 m= 16201 mr = 43261 m= 2607 mr = 11484 m= 254 mr = 1592 m= 8 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 67807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 18904 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) : 1.689312 object centre at (A) : 7.800500 3.826501 21.44450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5438887 -8.0120405E-03 midg,1,midg; midg,igrid,midg 0.2615498 -0.1183498 1,midg,midg; igrid,midg,midg -0.4304406 0.3701638 gauss-seidel spectral radius is 0.9991602 estimated iterations to convergence 273 setup time was (sec) 1.250000 now iterating at: 14:48:09 rms-change max change #iterations 8.277533 409.9759 at 10iterations 4.704484 115.3826 at 20iterations 2.657425 61.60896 at 30iterations 1.487653 38.60085 at 40iterations 0.8350430 18.08797 at 50iterations 0.4650776 11.46887 at 60iterations 0.2585974 6.209395 at 70iterations 0.1440225 3.161126 at 80iterations 7.9853550E-02 1.701733 at 90iterations 4.4426043E-02 0.9279404 at 100iterations 2.4676610E-02 0.5092186 at 110iterations 1.3674340E-02 0.2933407 at 120iterations 7.5607114E-03 0.1683350 at 130iterations 4.2099277E-03 0.1052227 at 140iterations 2.3365780E-03 5.3184509E-02 at 150iterations 1.2998130E-03 2.6375771E-02 at 160iterations 7.2409306E-04 1.5342712E-02 at 170iterations 4.0656494E-04 9.3116760E-03 at 180iterations finished qdiffx linear iterations at : 14:48:18 total time elapsed so far: 10.83000 # loops : 180 mean,max change (kT/e) : 4.0656494E-04 9.3116760E-03 energy calculations done at 10.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 14:48:19 11.012u 0.159s 0:11.49 97.1% 0+0k 0+0io 0pf+0w