Sun Oct 9 23:36:48 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 23:36:48 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 = 2810 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: 0.5324001 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 0.5324001 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.78313 89.68904 89.53252 assigned negative charge : -423.6726 centred at (gu) : 89.83899 89.78204 89.48361 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5134 nv = 96 ne = 84 npr = 53955 no. pairs analyzed = 53955 no. exposed pairs = 3732 no. arc points = 27581 no. surface atoms = 1239 nbur = 1571 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 = 1.596000 m= 178 mr = 2403 m= 0 mr = 5 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 2904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2828 ## 467 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9746231E-12 3.2286832E-10 midg,1,midg; midg,igrid,midg 5.6927441E-10 -1.6017565E-10 1,midg,midg; igrid,midg,midg 4.1079307E-10 -2.9540925E-11 gauss-seidel spectral radius is 0.9818149 estimated iterations to convergence 61 setup time was (sec) 0.3900000 now iterating at: 23:36:49 rms-change max change #iterations 6.1681684E-02 11.34095 at 10iterations 3.7578130E-03 0.6288385 at 20iterations 2.3972604E-04 5.0145864E-02 at 30iterations 1.4674676E-05 2.4528503E-03 at 40iterations 9.4781751E-07 1.7929077E-04 at 50iterations finished qdiffx linear iterations at : 23:36:52 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 9.4781751E-07 1.7929077E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 23:36:52 3.448u 0.169s 0:03.92 91.8% 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 23:36:52 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 = 2810 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: 1.597200 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 1.597200 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.34884 89.06666 88.59727 assigned negative charge : -423.6726 centred at (gu) : 89.51672 89.34583 88.45081 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 57050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 15678 mr = 36412 m= 1390 mr = 10221 m= 26 mr = 594 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.2900000 number of dielectric boundary points 26917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20297 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) : 0.5324001 object centre at (A) : -7.078501 -1.250999 14.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9785394E-03 1.8786613E-04 midg,1,midg; midg,igrid,midg 9.0229502E-03 2.0709694E-03 1,midg,midg; igrid,midg,midg 1.3358215E-02 3.2896462E-03 gauss-seidel spectral radius is 0.9980825 estimated iterations to convergence 181 setup time was (sec) 0.5000000 now iterating at: 23:36:53 rms-change max change #iterations 3.053972 144.6276 at 10iterations 1.229707 55.04572 at 20iterations 0.4986255 22.17152 at 30iterations 0.2022046 7.567175 at 40iterations 8.1942022E-02 3.277218 at 50iterations 3.3318304E-02 1.365913 at 60iterations 1.3515921E-02 0.5033150 at 70iterations 5.4930625E-03 0.2414474 at 80iterations 2.2321783E-03 8.6841583E-02 at 90iterations 9.0713426E-04 3.6267281E-02 at 100iterations 3.6777687E-04 1.3515234E-02 at 110iterations 1.4946311E-04 5.4626465E-03 at 120iterations finished qdiffx linear iterations at : 23:37:00 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.4946311E-04 5.4626465E-03 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 23:37:00 7.685u 0.192s 0:08.14 96.6% 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 23:37:00 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 = 2810 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: 2.395800 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 2.395800 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2668 net assigned charge : 5.000008 assigned positive charge : 428.6716 centred at (gu) : 89.02313 88.59966 87.89579 assigned negative charge : -423.6726 centred at (gu) : 89.27497 89.01872 87.67614 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 132601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55787 mr = 89627 m= 14202 mr = 42653 m= 2019 mr = 10343 m= 93 mr = 1225 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 4121 time to turn everything in is 0.6700000 number of dielectric boundary points 60846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21310 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) : 1.597200 object centre at (A) : -7.078501 -1.250999 14.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7799005E-02 2.1163854E-03 midg,1,midg; midg,igrid,midg 0.1313709 6.5747358E-02 1,midg,midg; igrid,midg,midg 9.5176175E-02 1.2482978E-02 gauss-seidel spectral radius is 0.9990992 estimated iterations to convergence 263 setup time was (sec) 0.8900000 now iterating at: 23:37:01 rms-change max change #iterations 7.921002 275.5195 at 10iterations 4.298663 102.5793 at 20iterations 2.341842 57.16426 at 30iterations 1.272851 31.49478 at 40iterations 0.6876277 15.91477 at 50iterations 0.3728197 8.988922 at 60iterations 0.2019747 5.148938 at 70iterations 0.1089021 2.392082 at 80iterations 5.8918849E-02 1.295778 at 90iterations 3.1881049E-02 0.7402802 at 100iterations 1.7239869E-02 0.4125433 at 110iterations 9.3176570E-03 0.2065125 at 120iterations 5.0255992E-03 0.1083345 at 130iterations 2.7178368E-03 5.9581280E-02 at 140iterations 1.4705778E-03 3.4878016E-02 at 150iterations 7.9570035E-04 1.8291056E-02 at 160iterations 4.2946730E-04 1.0175169E-02 at 170iterations 2.3223637E-04 5.3203106E-03 at 180iterations finished qdiffx linear iterations at : 23:37:12 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 2.3223637E-04 5.3203106E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 23:37:13 11.989u 0.215s 0:12.52 97.3% 0+0k 0+0io 0pf+0w