Mon Oct 10 00:55:22 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 Mon Oct 10 2011 at 00:55:22 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 = 2240 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: 0.6900696 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 0.6900696 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.000012 assigned positive charge : 331.7685 centred at (gu) : 88.69078 88.98692 89.75826 assigned negative charge : -326.7689 centred at (gu) : 88.56883 88.97630 89.75911 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 44273 no. pairs analyzed = 44273 no. exposed pairs = 3145 no. arc points = 21309 no. surface atoms = 1051 nbur = 1189 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 3961 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9978700E-08 2.6751659E-08 midg,1,midg; midg,igrid,midg 2.9920272E-08 2.6321425E-08 1,midg,midg; igrid,midg,midg -1.9612932E-08 5.4121156E-08 gauss-seidel spectral radius is 0.9890876 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 00:55:23 rms-change max change #iterations 0.1887790 28.27106 at 10iterations 2.1791955E-02 3.262939 at 20iterations 2.5878393E-03 0.3503265 at 30iterations 2.9943907E-04 3.5918236E-02 at 40iterations 3.6338410E-05 5.4845810E-03 at 50iterations finished qdiffx linear iterations at : 00:55:26 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.6338410E-05 5.4845810E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 00:55:26 3.342u 0.206s 0:03.87 91.4% 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 00:55:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 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: 2.070209 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 2.070209 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.000012 assigned positive charge : 331.7685 centred at (gu) : 86.07237 86.96056 89.27456 assigned negative charge : -326.7689 centred at (gu) : 85.70641 86.92875 89.27734 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 29823 mr = 53382 m= 5890 mr = 21732 m= 523 mr = 3864 m= 15 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 36081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16644 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) : 0.6900696 object centre at (A) : 16.49050 -27.84600 1.242001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3006364E-02 2.5414288E-02 midg,1,midg; midg,igrid,midg 1.1174523E-02 -1.9533027E-02 1,midg,midg; igrid,midg,midg 1.5557461E-02 4.1122977E-02 gauss-seidel spectral radius is 0.9988170 estimated iterations to convergence 230 setup time was (sec) 0.8700000 now iterating at: 00:55:27 rms-change max change #iterations 4.532982 191.6810 at 10iterations 2.233022 78.21095 at 20iterations 1.104316 40.62508 at 30iterations 0.5445349 20.54816 at 40iterations 0.2678602 8.449440 at 50iterations 0.1323511 3.892620 at 60iterations 6.4991489E-02 1.926668 at 70iterations 3.2321047E-02 0.9678202 at 80iterations 1.5899802E-02 0.4637222 at 90iterations 7.8666257E-03 0.2307415 at 100iterations 3.8699578E-03 0.1282654 at 110iterations 1.9171253E-03 6.0430527E-02 at 120iterations finished qdiffx linear iterations at : 00:55:34 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.9171253E-03 6.0430527E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 00:55:35 7.816u 0.237s 0:08.37 96.0% 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 00:55:35 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 = 2240 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: 3.105313 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 3.105313 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.000012 assigned positive charge : 331.7685 centred at (gu) : 84.10846 85.44083 88.91183 assigned negative charge : -326.7689 centred at (gu) : 83.55952 85.39317 88.91605 start vw surface at 0.1500000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 182432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 92939 mr = 129649 m= 37771 mr = 74898 m= 11261 mr = 30372 m= 2165 mr = 8709 m= 234 mr = 1489 m= 5 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 81567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 16784 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) : 2.070209 object centre at (A) : 16.49050 -27.84600 1.242001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9071481 0.2023149 midg,1,midg; midg,igrid,midg 6.8154246E-02 -0.3567684 1,midg,midg; igrid,midg,midg 0.2906223 0.3695185 gauss-seidel spectral radius is 0.9993107 estimated iterations to convergence 300 setup time was (sec) 2.110000 now iterating at: 00:55:37 rms-change max change #iterations 10.35553 378.0677 at 10iterations 6.211159 141.7701 at 20iterations 3.693970 85.07583 at 30iterations 2.190648 44.00489 at 40iterations 1.300930 22.30139 at 50iterations 0.7697543 15.91618 at 60iterations 0.4539819 8.692125 at 70iterations 0.2666506 5.384390 at 80iterations 0.1571277 3.003391 at 90iterations 9.2336841E-02 1.605717 at 100iterations 5.4295011E-02 1.010355 at 110iterations 3.1854030E-02 0.5820179 at 120iterations 1.8717686E-02 0.3100748 at 130iterations 1.0983980E-02 0.2015419 at 140iterations 6.4276131E-03 0.1093874 at 150iterations 3.7716175E-03 6.4135551E-02 at 160iterations 2.2195128E-03 3.8961411E-02 at 170iterations 1.2995682E-03 2.6366740E-02 at 180iterations finished qdiffx linear iterations at : 00:55:49 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 1.2995682E-03 2.6366740E-02 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 00:55:50 14.592u 0.262s 0:15.13 98.1% 0+0k 0+0io 0pf+0w