Mon Oct 10 16:20:36 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 Mon Oct 10 2011 at 16:20:36 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 0.5477766 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 0.5477766 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 452.3771 centred at (gu) : 89.74120 88.49514 88.36766 assigned negative charge : -437.3783 centred at (gu) : 89.87368 88.43251 88.36068 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5794 nv = 96 ne = 84 npr = 57247 no. pairs analyzed = 57247 no. exposed pairs = 4101 no. arc points = 30320 no. surface atoms = 1369 nbur = 1613 mkacc time = 0.1000000 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 = 1.568000 m= 240 mr = 2636 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3060 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4136646E-09 7.1289036E-10 midg,1,midg; midg,igrid,midg 7.9929813E-10 9.9822695E-10 1,midg,midg; igrid,midg,midg 2.0325353E-09 6.5085604E-11 gauss-seidel spectral radius is 0.9828277 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 16:20:36 rms-change max change #iterations 7.0717804E-02 12.25165 at 10iterations 4.7418303E-03 0.8220091 at 20iterations 3.2671468E-04 5.0373077E-02 at 30iterations 2.2886790E-05 3.4103394E-03 at 40iterations 1.8542944E-06 2.8991699E-04 at 50iterations finished qdiffx linear iterations at : 16:20:39 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.8542944E-06 2.8991699E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:20:40 3.469u 0.162s 0:03.90 92.8% 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 Mon Oct 10 2011 at 16:20:40 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 1.643330 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 1.643330 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 452.3771 centred at (gu) : 89.22297 85.48436 85.10220 assigned negative charge : -437.3783 centred at (gu) : 89.62077 85.29729 85.08190 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18554 mr = 39341 m= 1884 mr = 12146 m= 47 mr = 785 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 796 time to turn everything in is 0.3300000 number of dielectric boundary points 31493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21595 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) : 0.5477766 object centre at (A) : 112.5640 22.59100 57.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7386600E-02 1.2360558E-02 midg,1,midg; midg,igrid,midg 5.5136094E-03 2.4601599E-02 1,midg,midg; igrid,midg,midg 1.5523111E-02 1.2232096E-02 gauss-seidel spectral radius is 0.9982143 estimated iterations to convergence 188 setup time was (sec) 0.5500000 now iterating at: 16:20:40 rms-change max change #iterations 3.350700 158.4549 at 10iterations 1.386667 54.86784 at 20iterations 0.5801831 24.40091 at 30iterations 0.2430423 9.021216 at 40iterations 0.1011616 4.050169 at 50iterations 4.2366669E-02 1.578322 at 60iterations 1.7772196E-02 0.6469903 at 70iterations 7.4608852E-03 0.2813644 at 80iterations 3.1129033E-03 0.1154671 at 90iterations 1.3071557E-03 4.8175812E-02 at 100iterations 5.4776622E-04 2.2466660E-02 at 110iterations 2.2979593E-04 8.4457397E-03 at 120iterations finished qdiffx linear iterations at : 16:20:48 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 2.2979593E-04 8.4457397E-03 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 16:20:48 7.843u 0.188s 0:08.35 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 Mon Oct 10 2011 at 16:20:48 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: 238 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 2.464995 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): 80.06900 145.0590 ymin,ymax (A): -8.192000 53.37400 zmin,zma (A): 30.05600 84.31500 x,y,z range (A): 64.98999 61.56600 54.25900 scale (grids/A): 2.464995 object centre (A): 112.5640 22.59100 57.18550 number of atom coordinates read : 2982 total number of charged atoms : 2821 net assigned charge : 15.00002 assigned positive charge : 452.3771 centred at (gu) : 88.83424 83.22638 82.65319 assigned negative charge : -437.3783 centred at (gu) : 89.43113 82.94591 82.62271 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 146381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63230 mr = 96605 m= 18387 mr = 48141 m= 2776 mr = 13394 m= 135 mr = 1616 m= 0 mr = 24 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2634 time to turn everything in is 0.7700000 number of dielectric boundary points 71129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22545 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) : 1.643330 object centre at (A) : 112.5640 22.59100 57.18550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2592079 0.1524476 midg,1,midg; midg,igrid,midg 6.0622785E-02 0.3904786 1,midg,midg; igrid,midg,midg 8.9489177E-02 0.4345568 gauss-seidel spectral radius is 0.9991454 estimated iterations to convergence 270 setup time was (sec) 1.000000 now iterating at: 16:20:49 rms-change max change #iterations 8.651045 297.7904 at 10iterations 4.863169 130.2167 at 20iterations 2.722225 70.62240 at 30iterations 1.513912 33.46730 at 40iterations 0.8400252 18.05782 at 50iterations 0.4631448 10.29951 at 60iterations 0.2558015 5.730156 at 70iterations 0.1412813 3.500490 at 80iterations 7.7887870E-02 1.658073 at 90iterations 4.2941321E-02 0.9343567 at 100iterations 2.3587883E-02 0.4928856 at 110iterations 1.3012790E-02 0.2919731 at 120iterations 7.1418891E-03 0.1494141 at 130iterations 3.9331811E-03 8.0498695E-02 at 140iterations 2.1629098E-03 4.4435501E-02 at 150iterations 1.1907992E-03 2.2869110E-02 at 160iterations 6.5487809E-04 1.3898849E-02 at 170iterations 3.6015711E-04 7.9271793E-03 at 180iterations finished qdiffx linear iterations at : 16:21:01 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 3.6015711E-04 7.9271793E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 16:21:01 12.416u 0.208s 0:12.90 97.7% 0+0k 0+0io 0pf+0w