Sat Oct 8 17:24:51 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 Sat Oct 8 2011 at 17:24:51 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 = 3189 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: 0.5487814 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): -14.42200 42.96400 ymin,ymax (A): -39.57700 25.29400 zmin,zma (A): -14.51500 34.56200 x,y,z range (A): 57.38600 64.87100 49.07700 scale (grids/A): 0.5487814 object centre (A): 14.27100 -7.141500 10.02350 number of atom coordinates read : 3189 total number of charged atoms : 3045 net assigned charge : -3.499979 assigned positive charge : 475.7869 centred at (gu) : 90.85043 91.91995 90.00777 assigned negative charge : -479.2881 centred at (gu) : 90.82588 91.95415 89.98529 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6225 nv = 96 ne = 84 npr = 64487 no. pairs analyzed = 64487 no. exposed pairs = 3996 no. arc points = 27643 no. surface atoms = 1360 nbur = 1829 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 = 1.596000 m= 245 mr = 3285 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2820 ## 357 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1533657E-10 -6.0651748E-11 midg,1,midg; midg,igrid,midg 1.6237310E-11 -8.2023410E-10 1,midg,midg; igrid,midg,midg -3.5187264E-10 -5.1883695E-11 gauss-seidel spectral radius is 0.9828920 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 17:24:52 rms-change max change #iterations 7.8025460E-02 13.37510 at 10iterations 5.3465487E-03 0.8556280 at 20iterations 4.2789709E-04 6.7947388E-02 at 30iterations 6.3641222E-05 8.7842941E-03 at 40iterations 1.5079519E-05 2.0480156E-03 at 50iterations finished qdiffx linear iterations at : 17:24:54 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.5079519E-05 2.0480156E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:24:55 3.172u 0.146s 0:03.74 88.5% 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 Sat Oct 8 2011 at 17:24:55 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 = 3189 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: 1.646344 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): -14.42200 42.96400 ymin,ymax (A): -39.57700 25.29400 zmin,zma (A): -14.51500 34.56200 x,y,z range (A): 57.38600 64.87100 49.07700 scale (grids/A): 1.646344 object centre (A): 14.27100 -7.141500 10.02350 number of atom coordinates read : 3189 total number of charged atoms : 3045 net assigned charge : -3.499979 assigned positive charge : 475.7869 centred at (gu) : 92.55058 95.75904 90.02289 assigned negative charge : -479.2881 centred at (gu) : 92.47742 95.86200 89.95560 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21842 mr = 47457 m= 2248 mr = 15068 m= 61 mr = 1079 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 171 time to turn everything in is 0.4800000 number of dielectric boundary points 29430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 23334 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) : 0.5487814 object centre at (A) : 14.27100 -7.141500 10.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6483763E-03 1.9218946E-03 midg,1,midg; midg,igrid,midg 8.8606356E-03 -8.8703930E-03 1,midg,midg; igrid,midg,midg -8.8863843E-04 -6.5649594E-03 gauss-seidel spectral radius is 0.9982305 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 17:24:56 rms-change max change #iterations 3.491660 130.3631 at 10iterations 1.470206 63.42246 at 20iterations 0.6172447 23.36491 at 30iterations 0.2617702 8.819271 at 40iterations 0.1106009 4.003780 at 50iterations 4.6535570E-02 1.512328 at 60iterations 1.9747639E-02 0.7676239 at 70iterations 8.3482275E-03 0.2973127 at 80iterations 3.5401948E-03 0.1220976 at 90iterations 1.5005121E-03 5.3535938E-02 at 100iterations 6.3901447E-04 2.1958351E-02 at 110iterations 2.7780270E-04 1.0566711E-02 at 120iterations finished qdiffx linear iterations at : 17:25:02 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.7780270E-04 1.0566711E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:25:02 7.058u 0.194s 0:07.52 96.2% 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 Sat Oct 8 2011 at 17:25:02 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 = 3189 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: 2.469516 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): -14.42200 42.96400 ymin,ymax (A): -39.57700 25.29400 zmin,zma (A): -14.51500 34.56200 x,y,z range (A): 57.38600 64.87100 49.07700 scale (grids/A): 2.469516 object centre (A): 14.27100 -7.141500 10.02350 number of atom coordinates read : 3189 total number of charged atoms : 3045 net assigned charge : -3.499979 assigned positive charge : 475.7869 centred at (gu) : 93.82567 98.63823 90.03420 assigned negative charge : -479.2881 centred at (gu) : 93.71601 98.79292 89.93333 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 159968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 75538 mr = 115711 m= 21645 mr = 60116 m= 3486 mr = 16294 m= 261 mr = 2254 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 565 time to turn everything in is 1.180000 number of dielectric boundary points 66448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 24333 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) : 1.646344 object centre at (A) : 14.27100 -7.141500 10.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1220481 3.6535311E-02 midg,1,midg; midg,igrid,midg 0.3668280 -0.1582442 1,midg,midg; igrid,midg,midg 2.3093529E-02 -7.7496633E-02 gauss-seidel spectral radius is 0.9991520 estimated iterations to convergence 271 setup time was (sec) 1.490000 now iterating at: 17:25:04 rms-change max change #iterations 9.054538 313.4189 at 10iterations 5.119694 140.8133 at 20iterations 2.879294 85.57571 at 30iterations 1.613694 34.99865 at 40iterations 0.9013193 20.35297 at 50iterations 0.5013793 11.78789 at 60iterations 0.2783628 5.660718 at 70iterations 0.1547524 3.378128 at 80iterations 8.5645385E-02 1.808037 at 90iterations 4.7410619E-02 0.9047766 at 100iterations 2.6231728E-02 0.5195713 at 110iterations 1.4510735E-02 0.3353195 at 120iterations 8.0299461E-03 0.1731510 at 130iterations 4.4539622E-03 8.3953857E-02 at 140iterations 2.4619265E-03 4.8973560E-02 at 150iterations 1.3624791E-03 2.8501987E-02 at 160iterations 7.5659895E-04 1.4339447E-02 at 170iterations 4.2297118E-04 8.2168579E-03 at 180iterations finished qdiffx linear iterations at : 17:25:14 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 4.2297118E-04 8.2168579E-03 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 17:25:15 12.074u 0.199s 0:12.56 97.6% 0+0k 0+0io 0pf+0w