Mon Oct 10 14:09:02 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+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 14:09:02 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6156080 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 0.6156080 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 417.2575 centred at (gu) : 89.56037 89.83103 91.68102 assigned negative charge : -408.7581 centred at (gu) : 89.59473 89.82598 91.63422 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6932 nv = 96 ne = 84 npr = 54580 no. pairs analyzed = 54580 no. exposed pairs = 3668 no. arc points = 26279 no. surface atoms = 1228 nbur = 1533 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3558 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2657 ## 303 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8595 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1456366E-09 1.2677199E-08 midg,1,midg; midg,igrid,midg 5.7913687E-09 5.9855525E-09 1,midg,midg; igrid,midg,midg 8.8018330E-09 3.4497765E-09 gauss-seidel spectral radius is 0.9863557 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 14:09:03 rms-change max change #iterations 0.1284319 24.21163 at 10iterations 1.1484129E-02 1.747735 at 20iterations 1.0160393E-03 0.1495514 at 30iterations 9.5269381E-05 1.4266968E-02 at 40iterations 8.8571524E-06 1.2187958E-03 at 50iterations finished qdiffx linear iterations at : 14:09:06 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.8571524E-06 1.2187958E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:09:06 3.346u 0.189s 0:04.09 86.0% 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 14:09:06 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.846824 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 1.846824 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 417.2575 centred at (gu) : 88.68069 89.49242 95.04199 assigned negative charge : -408.7581 centred at (gu) : 88.78380 89.47749 94.90225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76176 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26279 grid for indexing accessible points = 1.400000 m= 25526 mr = 51272 m= 3592 mr = 17756 m= 212 mr = 1976 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3800000 number of dielectric boundary points 34432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20290 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) : 0.6156080 object centre at (A) : 32.01750 33.05900 30.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1290462E-02 3.2791164E-02 midg,1,midg; midg,igrid,midg 1.2734769E-02 1.7878525E-03 1,midg,midg; igrid,midg,midg 1.6642286E-02 2.4886648E-03 gauss-seidel spectral radius is 0.9985684 estimated iterations to convergence 210 setup time was (sec) 0.5900000 now iterating at: 14:09:07 rms-change max change #iterations 4.115945 187.5825 at 10iterations 1.893641 68.98297 at 20iterations 0.8690866 31.97433 at 30iterations 0.3966574 13.15262 at 40iterations 0.1829215 5.773827 at 50iterations 8.4171057E-02 2.675165 at 60iterations 3.8654007E-02 1.178448 at 70iterations 1.7784389E-02 0.5651779 at 80iterations 8.1922887E-03 0.2768326 at 90iterations 3.7695032E-03 0.1276159 at 100iterations 1.7414987E-03 5.8664322E-02 at 110iterations 8.0747693E-04 2.4309158E-02 at 120iterations finished qdiffx linear iterations at : 14:09:14 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 8.0747693E-04 2.4309158E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:09:15 7.769u 0.188s 0:08.45 93.9% 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 Mon Oct 10 2011 at 14:09:15 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.770236 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): 3.103000 60.93200 ymin,ymax (A): 4.704000 61.41400 zmin,zma (A): 6.688000 54.10300 x,y,z range (A): 57.82900 56.71000 47.41500 scale (grids/A): 2.770236 object centre (A): 32.01750 33.05900 30.39550 number of atom coordinates read : 2761 total number of charged atoms : 2588 net assigned charge : 8.500020 assigned positive charge : 417.2575 centred at (gu) : 88.02097 89.23850 97.56284 assigned negative charge : -408.7581 centred at (gu) : 88.17553 89.21622 97.35332 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 176347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26279 grid for indexing accessible points = 1.400000 m= 84609 mr = 125031 m= 27781 mr = 67246 m= 6053 mr = 21083 m= 900 mr = 4117 m= 41 mr = 565 m= 0 mr = 2 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 0.9500000 number of dielectric boundary points 77687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 20703 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) : 1.846824 object centre at (A) : 32.01750 33.05900 30.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1221729 0.3733468 midg,1,midg; midg,igrid,midg 0.4001410 9.9389004E-03 1,midg,midg; igrid,midg,midg 0.1644828 -5.6182995E-02 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 1.190000 now iterating at: 14:09:16 rms-change max change #iterations 9.949371 298.8909 at 10iterations 5.870745 143.1671 at 20iterations 3.429496 81.53789 at 30iterations 1.994018 45.22269 at 40iterations 1.156474 31.21218 at 50iterations 0.6680867 14.39229 at 60iterations 0.3854145 8.423855 at 70iterations 0.2222961 4.191320 at 80iterations 0.1277558 2.706768 at 90iterations 7.3390529E-02 1.560944 at 100iterations 4.2105801E-02 0.7834549 at 110iterations 2.4138857E-02 0.4408035 at 120iterations 1.3850762E-02 0.2466240 at 130iterations 7.9332162E-03 0.1531982 at 140iterations 4.5562563E-03 8.7286949E-02 at 150iterations 2.6088520E-03 4.9018860E-02 at 160iterations 1.4970513E-03 2.7507782E-02 at 170iterations 8.5705798E-04 1.7397881E-02 at 180iterations finished qdiffx linear iterations at : 14:09:28 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 8.5705798E-04 1.7397881E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 14:09:28 12.548u 0.205s 0:13.15 96.8% 0+0k 0+0io 0pf+0w