Sun Oct 9 14:15:17 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 14:15:17 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 = 2659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5665632 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 0.5665632 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.000018 assigned positive charge : 400.9884 centred at (gu) : 89.51820 90.26757 89.11101 assigned negative charge : -392.9894 centred at (gu) : 89.52023 90.16079 89.13983 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5573 nv = 96 ne = 84 npr = 52649 no. pairs analyzed = 52649 no. exposed pairs = 3433 no. arc points = 24078 no. surface atoms = 1148 nbur = 1511 mkacc time = 8.9999996E-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= 242 mr = 2810 m= 0 mr = 11 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2432 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7638473E-09 5.8900462E-10 midg,1,midg; midg,igrid,midg -2.3866381E-10 2.5323679E-09 1,midg,midg; igrid,midg,midg 1.2315557E-09 9.4030883E-10 gauss-seidel spectral radius is 0.9839028 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 14:15:18 rms-change max change #iterations 8.3451144E-02 17.74132 at 10iterations 6.0391775E-03 0.9155130 at 20iterations 4.4643556E-04 8.8996887E-02 at 30iterations 3.5172656E-05 5.8174133E-03 at 40iterations 3.4726929E-06 5.5694580E-04 at 50iterations finished qdiffx linear iterations at : 14:15:21 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 3.4726929E-06 5.5694580E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:15:21 3.442u 0.186s 0:03.90 92.8% 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 Sun Oct 9 2011 at 14:15:21 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 = 2659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.699690 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 1.699690 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.000018 assigned positive charge : 400.9884 centred at (gu) : 88.55392 90.80196 87.33250 assigned negative charge : -392.9894 centred at (gu) : 88.56039 90.48228 87.41904 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24078 grid for indexing accessible points = 1.400000 m= 19061 mr = 41617 m= 1969 mr = 12687 m= 73 mr = 860 m= 1 mr = 8 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 0.3100000 number of dielectric boundary points 27817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19433 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) : 0.5665632 object centre at (A) : 25.17300 15.74400 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3282840E-02 1.2230928E-02 midg,1,midg; midg,igrid,midg -5.8351510E-04 4.7254204E-03 1,midg,midg; igrid,midg,midg 2.7296778E-03 5.7351980E-03 gauss-seidel spectral radius is 0.9983041 estimated iterations to convergence 193 setup time was (sec) 0.5300000 now iterating at: 14:15:22 rms-change max change #iterations 3.370213 170.4337 at 10iterations 1.441001 58.31696 at 20iterations 0.6192642 23.35789 at 30iterations 0.2663401 10.32143 at 40iterations 0.1139578 4.181429 at 50iterations 4.8707038E-02 1.992058 at 60iterations 2.0999841E-02 0.7415905 at 70iterations 8.9990422E-03 0.3482513 at 80iterations 3.8652364E-03 0.1457920 at 90iterations 1.6586005E-03 6.1791420E-02 at 100iterations 7.1389822E-04 2.5033951E-02 at 110iterations 3.0833139E-04 1.1474609E-02 at 120iterations finished qdiffx linear iterations at : 14:15:29 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 3.0833139E-04 1.1474609E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 14:15:29 7.807u 0.221s 0:08.29 96.7% 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 14:15:29 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 = 2659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.549535 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 2.549535 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.000018 assigned positive charge : 400.9884 centred at (gu) : 87.83066 91.20288 85.99859 assigned negative charge : -392.9894 centred at (gu) : 87.84028 90.72323 86.12859 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24078 grid for indexing accessible points = 1.400000 m= 65786 mr = 101735 m= 18763 mr = 51270 m= 3091 mr = 13558 m= 298 mr = 1852 m= 9 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 62754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20145 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) : 1.699690 object centre at (A) : 25.17300 15.74400 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5849674 0.2032094 midg,1,midg; midg,igrid,midg -8.5048825E-03 7.4347765E-03 1,midg,midg; igrid,midg,midg 3.9180644E-02 4.6825904E-02 gauss-seidel spectral radius is 0.9991690 estimated iterations to convergence 274 setup time was (sec) 0.9900000 now iterating at: 14:15:31 rms-change max change #iterations 8.619765 308.0040 at 10iterations 4.939234 149.5100 at 20iterations 2.819038 79.02579 at 30iterations 1.590605 37.34649 at 40iterations 0.8981769 19.57886 at 50iterations 0.5034798 10.99236 at 60iterations 0.2826587 6.666348 at 70iterations 0.1580206 3.507235 at 80iterations 8.8442937E-02 1.997570 at 90iterations 4.9285445E-02 1.069647 at 100iterations 2.7501574E-02 0.5648661 at 110iterations 1.5305789E-02 0.3222713 at 120iterations 8.5391412E-03 0.1900120 at 130iterations 4.7494783E-03 9.8505020E-02 at 140iterations 2.6438737E-03 5.7447433E-02 at 150iterations 1.4684552E-03 2.9811859E-02 at 160iterations 8.2003453E-04 2.0221710E-02 at 170iterations 4.5590650E-04 9.7751617E-03 at 180iterations finished qdiffx linear iterations at : 14:15:42 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 4.5590650E-04 9.7751617E-03 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:15:42 12.324u 0.197s 0:12.82 97.5% 0+0k 0+0io 0pf+0w