Mon Oct 10 17:03:32 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+sph2.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 = amb2.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 17:03:33 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 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: 0.5297698 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): -16.29000 50.90900 ymin,ymax (A): -17.57200 26.87800 zmin,zma (A): -5.232000 41.92900 x,y,z range (A): 67.19900 44.45000 47.16100 scale (grids/A): 0.5297698 object centre (A): 17.30950 4.653000 18.34850 number of atom coordinates read : 2890 total number of charged atoms : 2748 net assigned charge : -2.499959 assigned positive charge : 436.9841 centred at (gu) : 89.57461 90.49162 90.60024 assigned negative charge : -439.4853 centred at (gu) : 89.57678 90.64105 90.74083 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5216 nv = 96 ne = 84 npr = 57524 no. pairs analyzed = 57524 no. exposed pairs = 3794 no. arc points = 26902 no. surface atoms = 1281 nbur = 1609 mkacc time = 0.1400000 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 = 1.624000 m= 189 mr = 2529 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 403 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5193026E-10 -6.7412553E-10 midg,1,midg; midg,igrid,midg 3.8838277E-10 -6.9212436E-10 1,midg,midg; igrid,midg,midg -7.3612769E-11 -7.3484697E-11 gauss-seidel spectral radius is 0.9816396 estimated iterations to convergence 61 setup time was (sec) 0.5700000 now iterating at: 17:03:33 rms-change max change #iterations 6.0993731E-02 13.53072 at 10iterations 3.7087209E-03 0.6617975 at 20iterations 2.2761607E-04 4.2333484E-02 at 30iterations 1.3739685E-05 2.2745132E-03 at 40iterations 8.5292390E-07 1.4686584E-04 at 50iterations finished qdiffx linear iterations at : 17:03:36 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 8.5292390E-07 1.4686584E-04 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 17:03:38 3.866u 0.175s 0:05.85 68.8% 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 Mon Oct 10 2011 at 17:03:39 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 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: 1.589309 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): -16.29000 50.90900 ymin,ymax (A): -17.57200 26.87800 zmin,zma (A): -5.232000 41.92900 x,y,z range (A): 67.19900 44.45000 47.16100 scale (grids/A): 1.589309 object centre (A): 17.30950 4.653000 18.34850 number of atom coordinates read : 2890 total number of charged atoms : 2748 net assigned charge : -2.499959 assigned positive charge : 436.9841 centred at (gu) : 88.72336 91.47405 91.79985 assigned negative charge : -439.4853 centred at (gu) : 88.72997 91.92274 92.22221 start vw surface at 0.2100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 58560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26902 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16185 mr = 38461 m= 1407 mr = 10530 m= 21 mr = 547 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 137 time to turn everything in is 0.5000000 number of dielectric boundary points 26635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 20852 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) : 0.5297698 object centre at (A) : 17.30950 4.653000 18.34850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7021926E-03 -1.3044087E-02 midg,1,midg; midg,igrid,midg 2.4928632E-03 -4.8228749E-03 1,midg,midg; igrid,midg,midg -9.2085119E-04 6.6777988E-04 gauss-seidel spectral radius is 0.9980704 estimated iterations to convergence 181 setup time was (sec) 0.8200000 now iterating at: 17:03:40 rms-change max change #iterations 3.070965 151.5618 at 10iterations 1.239210 57.04688 at 20iterations 0.5022759 20.45442 at 30iterations 0.2029139 9.176726 at 40iterations 8.2224801E-02 3.217297 at 50iterations 3.3273008E-02 1.180023 at 60iterations 1.3498647E-02 0.5470452 at 70iterations 5.4522320E-03 0.2238636 at 80iterations 2.2245534E-03 8.1190586E-02 at 90iterations 8.9878414E-04 3.7259102E-02 at 100iterations 3.6522682E-04 1.4175415E-02 at 110iterations 1.4875004E-04 5.5055618E-03 at 120iterations finished qdiffx linear iterations at : 17:03:48 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 1.4875004E-04 5.5055618E-03 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 17:03:49 8.836u 0.252s 0:09.88 91.9% 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 17:03:49 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 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: 2.383964 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): -16.29000 50.90900 ymin,ymax (A): -17.57200 26.87800 zmin,zma (A): -5.232000 41.92900 x,y,z range (A): 67.19900 44.45000 47.16100 scale (grids/A): 2.383964 object centre (A): 17.30950 4.653000 18.34850 number of atom coordinates read : 2890 total number of charged atoms : 2748 net assigned charge : -2.499959 assigned positive charge : 436.9841 centred at (gu) : 88.08475 92.21101 92.69977 assigned negative charge : -439.4853 centred at (gu) : 88.09479 92.88410 93.33315 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 136087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26902 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 58219 mr = 94771 m= 14719 mr = 44648 m= 1892 mr = 10479 m= 97 mr = 1062 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 1.100000 number of dielectric boundary points 60016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 21958 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) : 1.589309 object centre at (A) : 17.30950 4.653000 18.34850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3428342E-02 -0.1891121 midg,1,midg; midg,igrid,midg 2.8124325E-02 -5.6247883E-02 1,midg,midg; igrid,midg,midg -0.2893354 0.2666129 gauss-seidel spectral radius is 0.9991005 estimated iterations to convergence 263 setup time was (sec) 1.450000 now iterating at: 17:03:51 rms-change max change #iterations 8.204836 242.0085 at 10iterations 4.549089 121.7122 at 20iterations 2.514382 64.02669 at 30iterations 1.372204 31.63347 at 40iterations 0.7503120 18.42039 at 50iterations 0.4092207 9.915880 at 60iterations 0.2230138 5.851653 at 70iterations 0.1210292 2.532275 at 80iterations 6.5819219E-02 1.355467 at 90iterations 3.5695117E-02 0.8296833 at 100iterations 1.9329363E-02 0.4124908 at 110iterations 1.0469237E-02 0.2513915 at 120iterations 5.6811990E-03 0.1221056 at 130iterations 3.0757012E-03 6.5439224E-02 at 140iterations 1.6659786E-03 3.8434982E-02 at 150iterations 9.0240280E-04 1.9726992E-02 at 160iterations 4.8911071E-04 1.2263536E-02 at 170iterations 2.6530609E-04 6.3533783E-03 at 180iterations finished qdiffx linear iterations at : 17:04:02 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 2.6530609E-04 6.3533783E-03 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 17:04:03 13.197u 0.275s 0:14.27 94.3% 0+0k 0+0io 0pf+0w