Sun Oct 9 15:21:32 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 15:21:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5689 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: 0.5036786 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): 67.28500 137.9650 ymin,ymax (A): -6.095000 57.03700 zmin,zma (A): -3.319000 65.67500 x,y,z range (A): 70.68000 63.13200 68.99400 scale (grids/A): 0.5036786 object centre (A): 102.6250 25.47100 31.17800 number of atom coordinates read : 5689 total number of charged atoms : 5518 net assigned charge : -3.499956 assigned positive charge : 869.4451 centred at (gu) : 89.85357 90.71536 90.22772 assigned negative charge : -872.9530 centred at (gu) : 89.92892 90.65528 90.34010 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8839 nv = 96 ne = 84 npr = 117747 no. pairs analyzed = 117747 no. exposed pairs = 6405 no. arc points = 44519 no. surface atoms = 2162 nbur = 3527 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 = 1.708000 m= 284 mr = 4864 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3800000 number of dielectric boundary points 4246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4335 ## 645 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0980430E-10 -3.2437178E-10 midg,1,midg; midg,igrid,midg -1.4799613E-10 1.2572633E-10 1,midg,midg; igrid,midg,midg 1.4409232E-10 -2.0744732E-10 gauss-seidel spectral radius is 0.9798950 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 15:21:32 rms-change max change #iterations 7.0298135E-02 9.672134 at 10iterations 4.5160665E-03 0.6692657 at 20iterations 6.4211077E-04 7.1044922E-02 at 30iterations 1.6199972E-04 1.7499924E-02 at 40iterations 4.6271602E-05 4.7655106E-03 at 50iterations finished qdiffx linear iterations at : 15:21:35 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 4.6271602E-05 4.7655106E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:21:36 3.613u 0.170s 0:04.25 88.9% 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 15:21:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5689 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: 1.511036 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): 67.28500 137.9650 ymin,ymax (A): -6.095000 57.03700 zmin,zma (A): -3.319000 65.67500 x,y,z range (A): 70.68000 63.13200 68.99400 scale (grids/A): 1.511036 object centre (A): 102.6250 25.47100 31.17800 number of atom coordinates read : 5689 total number of charged atoms : 5518 net assigned charge : -3.499956 assigned positive charge : 869.4451 centred at (gu) : 89.55864 92.14359 90.68120 assigned negative charge : -872.9530 centred at (gu) : 89.78676 91.96593 91.02035 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 101281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44519 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 29176 mr = 72130 m= 2399 mr = 20071 m= 53 mr = 1063 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4154 time to turn everything in is 0.5200000 number of dielectric boundary points 39643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 602 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 41269 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) : 0.5036786 object centre at (A) : 102.6250 25.47100 31.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4809419E-03 -1.3652522E-05 midg,1,midg; midg,igrid,midg -9.9065127E-03 5.1726038E-03 1,midg,midg; igrid,midg,midg -1.9256981E-02 -1.0090755E-02 gauss-seidel spectral radius is 0.9981193 estimated iterations to convergence 183 setup time was (sec) 0.7400000 now iterating at: 15:21:37 rms-change max change #iterations 4.116463 167.1932 at 10iterations 1.687538 58.26117 at 20iterations 0.6922191 19.56754 at 30iterations 0.2851010 8.887028 at 40iterations 0.1176845 4.227901 at 50iterations 4.8377503E-02 1.889695 at 60iterations 1.9985233E-02 0.5574398 at 70iterations 8.2592964E-03 0.2495499 at 80iterations 3.4430900E-03 0.1083698 at 90iterations 1.4452899E-03 4.5846939E-02 at 100iterations 6.2390836E-04 1.7739296E-02 at 110iterations 2.8277782E-04 8.3122253E-03 at 120iterations finished qdiffx linear iterations at : 15:21:44 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 2.8277782E-04 8.3122253E-03 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 15:21:44 8.070u 0.185s 0:08.59 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 15:21:44 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 = 5689 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: 2.266553 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): 67.28500 137.9650 ymin,ymax (A): -6.095000 57.03700 zmin,zma (A): -3.319000 65.67500 x,y,z range (A): 70.68000 63.13200 68.99400 scale (grids/A): 2.266553 object centre (A): 102.6250 25.47100 31.17800 number of atom coordinates read : 5689 total number of charged atoms : 5518 net assigned charge : -3.499956 assigned positive charge : 869.4451 centred at (gu) : 89.33749 93.21501 91.02106 assigned negative charge : -872.9530 centred at (gu) : 89.68027 92.94850 91.53048 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 236913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44519 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 105575 mr = 177085 m= 26302 mr = 84162 m= 3497 mr = 19538 m= 165 mr = 2173 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 14093 time to turn everything in is 1.180000 number of dielectric boundary points 89449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 44005 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) : 1.511036 object centre at (A) : 102.6250 25.47100 31.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9685074E-02 0.1299191 midg,1,midg; midg,igrid,midg -0.2139188 0.1576394 1,midg,midg; igrid,midg,midg -0.5741786 0.1490510 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 1.430000 now iterating at: 15:21:46 rms-change max change #iterations 11.07833 243.9875 at 10iterations 6.331114 130.4588 at 20iterations 3.591212 100.1089 at 30iterations 2.024851 42.26329 at 40iterations 1.140703 22.31499 at 50iterations 0.6407560 11.82156 at 60iterations 0.3588730 7.438713 at 70iterations 0.2013078 3.435943 at 80iterations 0.1124109 2.107018 at 90iterations 6.2924400E-02 1.037405 at 100iterations 3.5075057E-02 0.5997515 at 110iterations 1.9608008E-02 0.3367558 at 120iterations 1.0955601E-02 0.1918106 at 130iterations 6.1152084E-03 0.1111579 at 140iterations 3.4182929E-03 5.6545258E-02 at 150iterations 1.9187495E-03 3.3532619E-02 at 160iterations 1.0783258E-03 1.8695831E-02 at 170iterations 6.1003864E-04 1.0799408E-02 at 180iterations finished qdiffx linear iterations at : 15:21:58 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 6.1003864E-04 1.0799408E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 15:21:58 13.170u 0.206s 0:13.66 97.8% 0+0k 0+0io 0pf+0w