Mon Oct 10 14:09:34 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 14:09:34 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 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: 0.5579150 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 0.5579150 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 607.8139 centred at (gu) : 88.60262 90.10984 90.70096 assigned negative charge : -610.3168 centred at (gu) : 88.64942 90.02901 90.66536 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8028 nv = 96 ne = 84 npr = 78603 no. pairs analyzed = 78603 no. exposed pairs = 5056 no. arc points = 34931 no. surface atoms = 1694 nbur = 2240 mkacc time = 0.2300000 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 = 1.512000 m= 353 mr = 4249 m= 0 mr = 20 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3548 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10524 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4506361E-10 2.8665176E-10 midg,1,midg; midg,igrid,midg -1.3734975E-09 8.9128838E-10 1,midg,midg; igrid,midg,midg 5.6525767E-10 -6.5893235E-10 gauss-seidel spectral radius is 0.9835043 estimated iterations to convergence 64 setup time was (sec) 0.7300000 now iterating at: 14:09:35 rms-change max change #iterations 9.6201725E-02 13.30329 at 10iterations 6.9305901E-03 0.9516487 at 20iterations 5.2520318E-04 8.9080334E-02 at 30iterations 5.0153780E-05 6.5841675E-03 at 40iterations 9.9938516E-06 1.4152527E-03 at 50iterations finished qdiffx linear iterations at : 14:09:38 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 9.9938516E-06 1.4152527E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 14:09:39 4.203u 0.257s 0:04.97 89.5% 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 14:09:39 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.673745 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 1.673745 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 607.8139 centred at (gu) : 85.80684 90.32838 92.10192 assigned negative charge : -610.3168 centred at (gu) : 85.94788 90.08643 91.99558 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 89699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34931 grid for indexing accessible points = 1.400000 m= 28739 mr = 62509 m= 3284 mr = 19630 m= 96 mr = 1620 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 0.7800000 number of dielectric boundary points 38048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 29152 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) : 0.5579150 object centre at (A) : -19.75800 -7.634499 -24.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8343946E-03 -3.1334553E-03 midg,1,midg; midg,igrid,midg -2.1005619E-02 4.3313955E-03 1,midg,midg; igrid,midg,midg -3.5729890E-03 3.1279963E-03 gauss-seidel spectral radius is 0.9983764 estimated iterations to convergence 197 setup time was (sec) 1.070000 now iterating at: 14:09:40 rms-change max change #iterations 4.194936 158.0915 at 10iterations 1.830814 58.05515 at 20iterations 0.8007582 23.65670 at 30iterations 0.3498631 10.53933 at 40iterations 0.1533454 5.126250 at 50iterations 6.7046374E-02 1.950296 at 60iterations 2.9382523E-02 0.9179955 at 70iterations 1.2886249E-02 0.3756752 at 80iterations 5.6548892E-03 0.1757805 at 90iterations 2.4714156E-03 7.7854156E-02 at 100iterations 1.0861309E-03 3.6602020E-02 at 110iterations 4.7728210E-04 1.5305519E-02 at 120iterations finished qdiffx linear iterations at : 14:09:49 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 4.7728210E-04 1.5305519E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 14:09:50 9.602u 0.306s 0:10.56 93.7% 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 14:09:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3934 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: 2.510618 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): -50.27900 10.76300 ymin,ymax (A): -39.53900 24.27000 zmin,zma (A): -50.25900 1.823000 x,y,z range (A): 61.04200 63.80900 52.08200 scale (grids/A): 2.510618 object centre (A): -19.75800 -7.634499 -24.21800 number of atom coordinates read : 3934 total number of charged atoms : 3789 net assigned charge : -2.499989 assigned positive charge : 607.8139 centred at (gu) : 83.70985 90.49223 93.15242 assigned negative charge : -610.3168 centred at (gu) : 83.92177 90.12960 92.99334 start vw surface at 0.1800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 208573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34931 grid for indexing accessible points = 1.400000 m= 98886 mr = 152838 m= 28991 mr = 78421 m= 5236 mr = 21296 m= 461 mr = 3458 m= 8 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 4255 time to turn everything in is 1.940000 number of dielectric boundary points 85925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 30275 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) : 1.673745 object centre at (A) : -19.75800 -7.634499 -24.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1087203 5.9372876E-03 midg,1,midg; midg,igrid,midg -0.3266734 -1.8736172E-03 1,midg,midg; igrid,midg,midg -0.2582575 6.6631451E-02 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.270000 now iterating at: 14:09:52 rms-change max change #iterations 10.88303 354.1796 at 10iterations 6.380544 153.6368 at 20iterations 3.707784 75.58989 at 30iterations 2.142591 43.40965 at 40iterations 1.237992 26.63681 at 50iterations 0.7096712 13.46674 at 60iterations 0.4068404 7.595302 at 70iterations 0.2326427 4.427314 at 80iterations 0.1329619 2.420830 at 90iterations 7.5537175E-02 1.398153 at 100iterations 4.3027651E-02 0.7313271 at 110iterations 2.4510659E-02 0.4433532 at 120iterations 1.3950703E-02 0.2376037 at 130iterations 7.9252943E-03 0.1300964 at 140iterations 4.5062611E-03 9.2981339E-02 at 150iterations 2.5586046E-03 4.6802521E-02 at 160iterations 1.4530828E-03 2.5862694E-02 at 170iterations 8.2456006E-04 1.4373779E-02 at 180iterations finished qdiffx linear iterations at : 14:10:06 total time elapsed so far: 16.30000 # loops : 180 mean,max change (kT/e) : 8.2456006E-04 1.4373779E-02 energy calculations done at 16.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.47000 DelPhi exited at 14:10:07 16.472u 0.317s 0:17.29 97.0% 0+0k 0+0io 0pf+0w