Mon Oct 10 17:16:50 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 17:16:50 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5132346 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 0.5132346 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4545 net assigned charge : 7.706036 assigned positive charge : 720.6765 centred at (gu) : 90.21650 90.46613 88.39308 assigned negative charge : -712.9748 centred at (gu) : 90.10313 90.52112 88.35774 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8095 nv = 96 ne = 84 npr = 96349 no. pairs analyzed = 96349 no. exposed pairs = 6159 no. arc points = 42970 no. surface atoms = 2053 nbur = 2742 mkacc time = 0.1600000 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 = 1.652000 m= 289 mr = 4168 m= 0 mr = 5 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4117 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10678 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0483900E-11 1.4953996E-10 midg,1,midg; midg,igrid,midg 2.4997387E-10 -4.0731540E-11 1,midg,midg; igrid,midg,midg -1.9574918E-10 4.7331783E-10 gauss-seidel spectral radius is 0.9805890 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 17:16:50 rms-change max change #iterations 7.0293173E-02 12.14882 at 10iterations 4.1825860E-03 0.6347790 at 20iterations 4.2728946E-04 5.8770657E-02 at 30iterations 1.3710681E-04 2.2352219E-02 at 40iterations 5.4903612E-05 1.0005474E-02 at 50iterations finished qdiffx linear iterations at : 17:16:53 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.4903612E-05 1.0005474E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:16:54 3.485u 0.160s 0:03.98 91.4% 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 Mon Oct 10 2011 at 17:16:54 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.539704 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 1.539704 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4545 net assigned charge : 7.706036 assigned positive charge : 720.6765 centred at (gu) : 90.64799 91.39703 85.17790 assigned negative charge : -712.9748 centred at (gu) : 90.30932 91.56332 85.07291 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 91533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26439 mr = 62658 m= 2270 mr = 17404 m= 44 mr = 879 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 39344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 568 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 34281 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) : 0.5132346 object centre at (A) : 9.469002 1.683501 30.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1428608E-03 2.2280553E-02 midg,1,midg; midg,igrid,midg 1.0511417E-02 -1.2962648E-02 1,midg,midg; igrid,midg,midg -1.3168069E-03 1.1305239E-02 gauss-seidel spectral radius is 0.9981425 estimated iterations to convergence 184 setup time was (sec) 0.6500000 now iterating at: 17:16:55 rms-change max change #iterations 3.851323 175.5349 at 10iterations 1.583034 63.47723 at 20iterations 0.6562831 21.18759 at 30iterations 0.2710896 8.740503 at 40iterations 0.1122360 3.552181 at 50iterations 4.6520654E-02 1.639636 at 60iterations 1.9226672E-02 0.6446152 at 70iterations 7.9712467E-03 0.2478886 at 80iterations 3.3142057E-03 0.1103797 at 90iterations 1.3885817E-03 4.5877457E-02 at 100iterations 5.9467711E-04 2.2242069E-02 at 110iterations 2.6945811E-04 1.0398269E-02 at 120iterations finished qdiffx linear iterations at : 17:17:02 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.6945811E-04 1.0398269E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 17:17:02 7.830u 0.184s 0:08.45 94.7% 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 Mon Oct 10 2011 at 17:17:02 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.309556 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): -17.91800 36.85600 ymin,ymax (A): -30.68300 34.05000 zmin,zma (A): -3.864000 65.50000 x,y,z range (A): 54.77400 64.73300 69.36400 scale (grids/A): 2.309556 object centre (A): 9.469002 1.683501 30.81800 number of atom coordinates read : 4795 total number of charged atoms : 4545 net assigned charge : 7.706036 assigned positive charge : 720.6765 centred at (gu) : 90.97169 92.09518 82.76656 assigned negative charge : -712.9748 centred at (gu) : 90.46385 92.34470 82.60933 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 213260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95113 mr = 154329 m= 23847 mr = 73921 m= 3157 mr = 16639 m= 149 mr = 1825 m= 0 mr = 43 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 88769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 36281 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) : 1.539704 object centre at (A) : 9.469002 1.683501 30.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1038597 0.5208939 midg,1,midg; midg,igrid,midg 0.2422721 -0.2906126 1,midg,midg; igrid,midg,midg -1.4219862E-02 0.1614962 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.310000 now iterating at: 17:17:04 rms-change max change #iterations 10.42958 284.9490 at 10iterations 6.007159 163.6819 at 20iterations 3.437331 89.90706 at 30iterations 1.959425 41.56707 at 40iterations 1.109312 25.00349 at 50iterations 0.6258866 14.49701 at 60iterations 0.3525302 7.114320 at 70iterations 0.1986097 4.105570 at 80iterations 0.1113473 2.292671 at 90iterations 6.2398084E-02 1.305897 at 100iterations 3.4969870E-02 0.6674347 at 110iterations 1.9608401E-02 0.3931274 at 120iterations 1.0966472E-02 0.2257843 at 130iterations 6.1375457E-03 0.1382961 at 140iterations 3.4281064E-03 6.4297199E-02 at 150iterations 1.9233944E-03 4.2195797E-02 at 160iterations 1.0835078E-03 2.0032883E-02 at 170iterations 6.1278185E-04 1.1468106E-02 at 180iterations finished qdiffx linear iterations at : 17:17:15 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 6.1278185E-04 1.1468106E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 17:17:16 12.882u 0.200s 0:13.40 97.6% 0+0k 0+0io 0pf+0w