Sun Oct 9 10:38:02 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 10:38:02 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 = 2658 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: 0.6392645 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 0.6392645 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 379.7105 centred at (gu) : 87.47445 90.24373 90.17580 assigned negative charge : -382.2118 centred at (gu) : 87.39104 90.20747 90.35278 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 53012 no. pairs analyzed = 53012 no. exposed pairs = 3768 no. arc points = 26829 no. surface atoms = 1266 nbur = 1392 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3787 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3200000 number of dielectric boundary points 4188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2450 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5557198E-08 -2.4292856E-08 midg,1,midg; midg,igrid,midg -6.9218205E-09 8.6656116E-10 1,midg,midg; igrid,midg,midg -2.1939375E-08 3.4323993E-09 gauss-seidel spectral radius is 0.9873461 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 10:38:03 rms-change max change #iterations 0.1451325 24.63103 at 10iterations 1.4230972E-02 1.863380 at 20iterations 1.4631953E-03 0.2014465 at 30iterations 1.9345514E-04 3.5758972E-02 at 40iterations 4.4980421E-05 8.6269379E-03 at 50iterations finished qdiffx linear iterations at : 10:38:05 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 4.4980421E-05 8.6269379E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:38:06 3.353u 0.161s 0:03.79 92.6% 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 10:38:06 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 = 2658 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: 1.917794 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 1.917794 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 379.7105 centred at (gu) : 82.42262 90.73040 90.52691 assigned negative charge : -382.2118 centred at (gu) : 82.17314 90.62239 91.05846 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 grid for indexing accessible points = 1.400000 m= 29753 mr = 52440 m= 5422 mr = 21315 m= 329 mr = 3378 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 869 time to turn everything in is 0.6400000 number of dielectric boundary points 38599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19876 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) : 0.6392645 object centre at (A) : 24.07450 29.09700 43.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0583552E-02 -2.5038512E-02 midg,1,midg; midg,igrid,midg -5.7872577E-04 3.0746456E-02 1,midg,midg; igrid,midg,midg -2.7602806E-03 -8.2391389E-03 gauss-seidel spectral radius is 0.9986888 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 10:38:07 rms-change max change #iterations 4.245748 201.1258 at 10iterations 2.005334 68.74490 at 20iterations 0.9519298 29.41833 at 30iterations 0.4533242 14.19063 at 40iterations 0.2143750 6.371237 at 50iterations 0.1023742 3.070808 at 60iterations 4.8641577E-02 1.534491 at 70iterations 2.3097331E-02 0.7418518 at 80iterations 1.0953472E-02 0.3188457 at 90iterations 5.2278391E-03 0.1606615 at 100iterations 2.4950237E-03 7.4220181E-02 at 110iterations 1.1907518E-03 3.5900116E-02 at 120iterations finished qdiffx linear iterations at : 10:38:14 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 1.1907518E-03 3.5900116E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 10:38:15 8.589u 0.280s 0:09.30 95.2% 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 Sun Oct 9 2011 at 10:38:15 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 = 2658 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: 2.876690 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): -3.770000 51.91900 ymin,ymax (A): 3.788000 54.40600 zmin,zma (A): 17.50800 69.04200 x,y,z range (A): 55.68900 50.61800 51.53400 scale (grids/A): 2.876690 object centre (A): 24.07450 29.09700 43.27500 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : -2.499978 assigned positive charge : 379.7105 centred at (gu) : 78.63362 91.09544 90.79009 assigned negative charge : -382.2118 centred at (gu) : 78.25981 90.93356 91.58762 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 185075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26829 grid for indexing accessible points = 1.400000 m= 93008 mr = 127751 m= 36656 mr = 74019 m= 9966 mr = 29093 m= 1501 mr = 7402 m= 66 mr = 926 m= 0 mr = 13 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2856 time to turn everything in is 1.620000 number of dielectric boundary points 87068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 20127 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) : 1.917794 object centre at (A) : 24.07450 29.09700 43.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2185356 -0.1570462 midg,1,midg; midg,igrid,midg 3.3568755E-02 0.3999189 1,midg,midg; igrid,midg,midg 0.2945819 -0.1799033 gauss-seidel spectral radius is 0.9992981 estimated iterations to convergence 298 setup time was (sec) 1.990000 now iterating at: 10:38:17 rms-change max change #iterations 10.20108 469.8297 at 10iterations 6.098985 135.2846 at 20iterations 3.645292 76.27107 at 30iterations 2.162407 41.96322 at 40iterations 1.278743 22.80233 at 50iterations 0.7519102 15.66557 at 60iterations 0.4419299 7.810154 at 70iterations 0.2600459 5.003646 at 80iterations 0.1522130 2.836082 at 90iterations 8.9102052E-02 1.602958 at 100iterations 5.2303854E-02 1.033356 at 110iterations 3.0514250E-02 0.5192480 at 120iterations 1.7798262E-02 0.3264787 at 130iterations 1.0437061E-02 0.1842175 at 140iterations 6.0888627E-03 0.1122684 at 150iterations 3.5478007E-03 7.3774382E-02 at 160iterations 2.0747562E-03 4.0763855E-02 at 170iterations 1.2114233E-03 2.1823883E-02 at 180iterations finished qdiffx linear iterations at : 10:38:30 total time elapsed so far: 14.38000 # loops : 180 mean,max change (kT/e) : 1.2114233E-03 2.1823883E-02 energy calculations done at 14.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.58000 DelPhi exited at 10:38:30 14.578u 0.271s 0:15.15 97.9% 0+0k 0+0io 0pf+0w