Mon Oct 10 14:06:53 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 14:06:53 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7275403 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): -7.506000 35.45900 ymin,ymax (A): -1.904000 47.02800 zmin,zma (A): -20.29800 21.44400 x,y,z range (A): 42.96500 48.93200 41.74200 scale (grids/A): 0.7275403 object centre (A): 13.97650 22.56200 0.5730000 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 273.9583 centred at (gu) : 90.27884 90.91285 89.21793 assigned negative charge : -275.9582 centred at (gu) : 90.22668 90.91842 89.33511 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 39078 no. pairs analyzed = 39078 no. exposed pairs = 2315 no. arc points = 16670 no. surface atoms = 775 nbur = 1114 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 3747 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 206 time to turn everything in is 0.1600000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1452 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9528897E-08 -9.2635716E-08 midg,1,midg; midg,igrid,midg -2.0101467E-08 -3.7003179E-08 1,midg,midg; igrid,midg,midg -5.9659364E-08 8.1282234E-09 gauss-seidel spectral radius is 0.9901339 estimated iterations to convergence 82 setup time was (sec) 0.3400000 now iterating at: 14:06:53 rms-change max change #iterations 0.2065521 27.46398 at 10iterations 2.7351053E-02 3.454719 at 20iterations 3.5606946E-03 0.4695148 at 30iterations 4.6237322E-04 6.3534737E-02 at 40iterations 5.9604339E-05 8.5754395E-03 at 50iterations finished qdiffx linear iterations at : 14:06:56 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.9604339E-05 8.5754395E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:06:57 3.354u 0.192s 0:04.01 88.2% 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 14:06:57 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.182621 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): -7.506000 35.45900 ymin,ymax (A): -1.904000 47.02800 zmin,zma (A): -20.29800 21.44400 x,y,z range (A): 42.96500 48.93200 41.74200 scale (grids/A): 2.182621 object centre (A): 13.97650 22.56200 0.5730000 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 273.9583 centred at (gu) : 90.83679 92.73872 87.65423 assigned negative charge : -275.9582 centred at (gu) : 90.68016 92.75553 88.00567 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 72095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16670 grid for indexing accessible points = 1.400000 m= 27455 mr = 50006 m= 5293 mr = 20569 m= 554 mr = 3483 m= 24 mr = 317 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 5584 time to turn everything in is 0.3500000 number of dielectric boundary points 31042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13985 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) : 0.7275403 object centre at (A) : 13.97650 22.56200 0.5730000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4172777E-02 -2.0554874E-02 midg,1,midg; midg,igrid,midg -3.1949216E-03 -1.2674816E-02 1,midg,midg; igrid,midg,midg -8.5226661E-03 -7.6015415E-03 gauss-seidel spectral radius is 0.9988748 estimated iterations to convergence 236 setup time was (sec) 0.5700000 now iterating at: 14:06:58 rms-change max change #iterations 4.558642 258.5907 at 10iterations 2.283881 75.77747 at 20iterations 1.146731 39.21763 at 30iterations 0.5732160 19.67324 at 40iterations 0.2886998 10.50128 at 50iterations 0.1453372 4.232105 at 60iterations 7.2802432E-02 2.042683 at 70iterations 3.6494561E-02 1.152481 at 80iterations 1.8350372E-02 0.6047459 at 90iterations 9.1966325E-03 0.2755127 at 100iterations 4.6095387E-03 0.1394720 at 110iterations 2.3220757E-03 8.2758904E-02 at 120iterations finished qdiffx linear iterations at : 14:07:05 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.3220757E-03 8.2758904E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 14:07:05 7.818u 0.208s 0:08.36 95.8% 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 14:07:06 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: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.273931 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): -7.506000 35.45900 ymin,ymax (A): -1.904000 47.02800 zmin,zma (A): -20.29800 21.44400 x,y,z range (A): 42.96500 48.93200 41.74200 scale (grids/A): 3.273931 object centre (A): 13.97650 22.56200 0.5730000 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 273.9583 centred at (gu) : 91.25520 94.10820 86.48135 assigned negative charge : -275.9582 centred at (gu) : 91.02026 94.13336 87.00850 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 166291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16670 grid for indexing accessible points = 1.400000 m= 85818 mr = 120535 m= 34423 mr = 70670 m= 10075 mr = 28262 m= 2217 mr = 7771 m= 325 mr = 1701 m= 23 mr = 225 m= 0 mr = 3 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 18777 time to turn everything in is 1.080000 number of dielectric boundary points 70005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14064 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) : 2.182621 object centre at (A) : 13.97650 22.56200 0.5730000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1517593 -0.1467152 midg,1,midg; midg,igrid,midg 0.1482522 -0.1262627 1,midg,midg; igrid,midg,midg 1.2586100E-03 -8.4925748E-02 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.300000 now iterating at: 14:07:07 rms-change max change #iterations 9.873605 432.4054 at 10iterations 5.786805 144.6888 at 20iterations 3.366920 70.82905 at 30iterations 1.966563 38.21062 at 40iterations 1.148719 20.19517 at 50iterations 0.6679618 13.28086 at 60iterations 0.3899893 7.152512 at 70iterations 0.2275496 3.905586 at 80iterations 0.1328135 2.366403 at 90iterations 7.7201627E-02 1.408360 at 100iterations 4.4991732E-02 0.8229209 at 110iterations 2.6188716E-02 0.4446607 at 120iterations 1.5267162E-02 0.2839775 at 130iterations 8.8904481E-03 0.1524386 at 140iterations 5.1791160E-03 8.9380264E-02 at 150iterations 3.0179718E-03 5.1300049E-02 at 160iterations 1.7590547E-03 2.8594971E-02 at 170iterations 1.0248494E-03 1.7247200E-02 at 180iterations finished qdiffx linear iterations at : 14:07:19 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.0248494E-03 1.7247200E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 14:07:19 12.624u 0.241s 0:13.36 96.2% 0+0k 0+0io 0pf+0w