Sun Oct 9 15:42:19 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 15:42:19 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5057464 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): 8.063001 61.79900 ymin,ymax (A): 56.15200 126.5430 zmin,zma (A): 29.18900 96.63900 x,y,z range (A): 53.73600 70.39101 67.45000 scale (grids/A): 0.5057464 object centre (A): 34.93100 91.34750 62.91400 number of atom coordinates read : 5523 total number of charged atoms : 5357 net assigned charge : 4.100031 assigned positive charge : 861.5901 centred at (gu) : 89.52715 89.56320 90.62641 assigned negative charge : -857.4979 centred at (gu) : 89.54206 89.53475 90.50702 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8453 nv = 96 ne = 84 npr = 112697 no. pairs analyzed = 112697 no. exposed pairs = 6559 no. arc points = 45220 no. surface atoms = 2187 nbur = 3336 mkacc time = 0.1900000 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 = 1.680000 m= 306 mr = 4521 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3700000 number of dielectric boundary points 4233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4333 ## 677 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2075164E-10 4.0454984E-10 midg,1,midg; midg,igrid,midg -3.0938262E-11 1.0379693E-10 1,midg,midg; igrid,midg,midg 9.3498924E-11 6.5241215E-12 gauss-seidel spectral radius is 0.9800448 estimated iterations to convergence 59 setup time was (sec) 0.5600000 now iterating at: 15:42:20 rms-change max change #iterations 7.0801489E-02 9.922745 at 10iterations 4.7559142E-03 0.6845627 at 20iterations 8.8633958E-04 0.1261368 at 30iterations 2.8565552E-04 3.9789200E-02 at 40iterations 9.7805649E-05 1.3525009E-02 at 50iterations finished qdiffx linear iterations at : 15:42:22 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 9.7805649E-05 1.3525009E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 15:42:23 3.627u 0.182s 0:04.22 90.0% 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 15:42:23 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.517239 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): 8.063001 61.79900 ymin,ymax (A): 56.15200 126.5430 zmin,zma (A): 29.18900 96.63900 x,y,z range (A): 53.73600 70.39101 67.45000 scale (grids/A): 1.517239 object centre (A): 34.93100 91.34750 62.91400 number of atom coordinates read : 5523 total number of charged atoms : 5357 net assigned charge : 4.100031 assigned positive charge : 861.5901 centred at (gu) : 88.57935 88.68756 91.87794 assigned negative charge : -857.4979 centred at (gu) : 88.62621 88.60378 91.52122 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 96957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45220 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27572 mr = 67610 m= 2250 mr = 18639 m= 52 mr = 984 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2392 time to turn everything in is 0.4900000 number of dielectric boundary points 39595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 682 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 40041 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) : 0.5057464 object centre at (A) : 34.93100 91.34750 62.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5112026E-02 1.4181551E-02 midg,1,midg; midg,igrid,midg -8.5646324E-03 1.2099957E-03 1,midg,midg; igrid,midg,midg 3.9234692E-03 3.4110029E-03 gauss-seidel spectral radius is 0.9981169 estimated iterations to convergence 183 setup time was (sec) 0.7100000 now iterating at: 15:42:24 rms-change max change #iterations 4.118830 167.1011 at 10iterations 1.686176 63.18269 at 20iterations 0.6925057 20.90234 at 30iterations 0.2851287 9.266968 at 40iterations 0.1170510 4.237877 at 50iterations 4.8497740E-02 1.471457 at 60iterations 2.0059817E-02 0.6498890 at 70iterations 8.3593503E-03 0.2671614 at 80iterations 3.5716828E-03 0.1147804 at 90iterations 1.6084726E-03 5.4620147E-02 at 100iterations 7.9579279E-04 2.4778366E-02 at 110iterations 4.4725105E-04 1.4796257E-02 at 120iterations finished qdiffx linear iterations at : 15:42:31 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 4.4725105E-04 1.4796257E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 15:42:32 8.055u 0.193s 0:08.58 96.0% 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 15:42:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5523 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.275859 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): 8.063001 61.79900 ymin,ymax (A): 56.15200 126.5430 zmin,zma (A): 29.18900 96.63900 x,y,z range (A): 53.73600 70.39101 67.45000 scale (grids/A): 2.275859 object centre (A): 34.93100 91.34750 62.91400 number of atom coordinates read : 5523 total number of charged atoms : 5357 net assigned charge : 4.100031 assigned positive charge : 861.5901 centred at (gu) : 87.86848 88.03083 92.81629 assigned negative charge : -857.4979 centred at (gu) : 87.93922 87.90562 92.28183 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 226874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45220 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 99204 mr = 166749 m= 24501 mr = 77894 m= 3239 mr = 17957 m= 132 mr = 2004 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 7994 time to turn everything in is 1.130000 number of dielectric boundary points 89311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 42711 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) : 1.517239 object centre at (A) : 34.93100 91.34750 62.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2392906 0.1089832 midg,1,midg; midg,igrid,midg -7.1915366E-02 -2.2954482E-03 1,midg,midg; igrid,midg,midg 7.3075667E-02 6.9279715E-02 gauss-seidel spectral radius is 0.9991706 estimated iterations to convergence 274 setup time was (sec) 1.380000 now iterating at: 15:42:33 rms-change max change #iterations 11.13786 345.6420 at 10iterations 6.323590 155.6502 at 20iterations 3.596297 76.82555 at 30iterations 2.033341 42.44836 at 40iterations 1.144992 22.65452 at 50iterations 0.6416008 12.01641 at 60iterations 0.3603664 6.626189 at 70iterations 0.2022004 3.845335 at 80iterations 0.1130110 2.262426 at 90iterations 6.3098624E-02 1.092583 at 100iterations 3.5289727E-02 0.6552429 at 110iterations 1.9658137E-02 0.3576427 at 120iterations 1.0957973E-02 0.2048950 at 130iterations 6.1245407E-03 0.1043730 at 140iterations 3.4125445E-03 6.4038277E-02 at 150iterations 1.9019879E-03 3.6865234E-02 at 160iterations 1.0615754E-03 1.9276142E-02 at 170iterations 5.9373182E-04 1.1489868E-02 at 180iterations finished qdiffx linear iterations at : 15:42:45 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 5.9373182E-04 1.1489868E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 15:42:46 13.288u 0.221s 0:13.88 97.2% 0+0k 0+0io 0pf+0w