Sun Oct 9 22:14:17 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 Sun Oct 9 2011 at 22:14:17 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6435286 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 0.6435286 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2433 net assigned charge : 4.525008 assigned positive charge : 390.1029 centred at (gu) : 89.94173 88.86810 90.17288 assigned negative charge : -385.5786 centred at (gu) : 89.90943 88.78428 90.20984 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6983 nv = 96 ne = 84 npr = 52680 no. pairs analyzed = 52680 no. exposed pairs = 3089 no. arc points = 22182 no. surface atoms = 1046 nbur = 1533 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3821 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.3200000 number of dielectric boundary points 3513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8561 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1688959E-08 2.7942393E-09 midg,1,midg; midg,igrid,midg -4.4084967E-09 1.4186038E-08 1,midg,midg; igrid,midg,midg 3.3412648E-09 1.1391339E-08 gauss-seidel spectral radius is 0.9874876 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 22:14:18 rms-change max change #iterations 0.1496454 24.71782 at 10iterations 1.5052234E-02 2.512752 at 20iterations 1.5118420E-03 0.2101092 at 30iterations 1.5001283E-04 2.0310640E-02 at 40iterations 1.5103342E-05 2.2439957E-03 at 50iterations finished qdiffx linear iterations at : 22:14:21 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.5103342E-05 2.2439957E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 22:14:21 3.485u 0.184s 0:03.94 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 Sun Oct 9 2011 at 22:14:21 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.930586 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 1.930586 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2433 net assigned charge : 4.525008 assigned positive charge : 390.1029 centred at (gu) : 89.82469 86.60385 90.51823 assigned negative charge : -385.5786 centred at (gu) : 89.72803 86.35255 90.62928 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22182 grid for indexing accessible points = 1.400000 m= 25690 mr = 52074 m= 3990 mr = 18672 m= 267 mr = 2466 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1653 time to turn everything in is 0.5800000 number of dielectric boundary points 32451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19169 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) : 0.6435286 object centre at (A) : 11.90500 10.73500 22.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4620848E-02 -9.8532224E-03 midg,1,midg; midg,igrid,midg 1.2723545E-02 -1.1563581E-02 1,midg,midg; igrid,midg,midg 1.0419479E-02 1.0905701E-03 gauss-seidel spectral radius is 0.9986634 estimated iterations to convergence 217 setup time was (sec) 0.8800000 now iterating at: 22:14:22 rms-change max change #iterations 4.310793 190.8499 at 10iterations 2.037655 66.83211 at 20iterations 0.9634195 32.04074 at 30iterations 0.4533867 15.25901 at 40iterations 0.2136427 7.023336 at 50iterations 0.1005247 3.424755 at 60iterations 4.7489353E-02 1.558808 at 70iterations 2.2381002E-02 0.7510166 at 80iterations 1.0565103E-02 0.3301153 at 90iterations 4.9906163E-03 0.1701050 at 100iterations 2.3491164E-03 7.8360558E-02 at 110iterations 1.1093188E-03 3.7387848E-02 at 120iterations finished qdiffx linear iterations at : 22:14:30 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 1.1093188E-03 3.7387848E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 22:14:30 8.388u 0.229s 0:08.97 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 Sun Oct 9 2011 at 22:14:30 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.895879 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 2.895879 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2433 net assigned charge : 4.525008 assigned positive charge : 390.1029 centred at (gu) : 89.73708 84.90578 90.77710 assigned negative charge : -385.5786 centred at (gu) : 89.59201 84.52869 90.94389 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 175665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22182 grid for indexing accessible points = 1.400000 m= 84631 mr = 126446 m= 29102 mr = 68841 m= 7119 mr = 23061 m= 1092 mr = 5409 m= 74 mr = 833 m= 0 mr = 37 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 5815 time to turn everything in is 1.460000 number of dielectric boundary points 73056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 19462 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) : 1.930586 object centre at (A) : 11.90500 10.73500 22.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4763439 -0.2722726 midg,1,midg; midg,igrid,midg 0.1696540 -0.1933833 1,midg,midg; igrid,midg,midg -7.5096600E-02 0.1075842 gauss-seidel spectral radius is 0.9992682 estimated iterations to convergence 292 setup time was (sec) 1.780000 now iterating at: 22:14:32 rms-change max change #iterations 10.02897 339.2202 at 10iterations 5.828466 133.3293 at 20iterations 3.371236 62.98054 at 30iterations 1.945853 39.07508 at 40iterations 1.122467 20.88859 at 50iterations 0.6462477 11.31164 at 60iterations 0.3725555 6.412506 at 70iterations 0.2146336 4.242607 at 80iterations 0.1235204 2.214851 at 90iterations 7.1134634E-02 1.346851 at 100iterations 4.0938471E-02 0.7125424 at 110iterations 2.3519192E-02 0.3903487 at 120iterations 1.3557559E-02 0.2684085 at 130iterations 7.7969106E-03 0.1384993 at 140iterations 4.4888570E-03 8.6026430E-02 at 150iterations 2.5833375E-03 4.9026012E-02 at 160iterations 1.4861299E-03 2.4795532E-02 at 170iterations 8.5677725E-04 1.6458511E-02 at 180iterations finished qdiffx linear iterations at : 22:14:44 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 8.5677725E-04 1.6458511E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 22:14:45 13.859u 0.231s 0:14.52 96.9% 0+0k 0+0io 0pf+0w