Sat Oct 8 16:52:46 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 Sat Oct 8 2011 at 16:52:46 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3579 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: 0.5582825 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 0.5582825 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 545.7455 centred at (gu) : 91.41293 89.29662 88.17991 assigned negative charge : -546.2469 centred at (gu) : 91.38367 89.14208 88.22345 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 70129 no. pairs analyzed = 70129 no. exposed pairs = 4766 no. arc points = 33098 no. surface atoms = 1594 nbur = 1985 mkacc time = 0.1600000 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= 345 mr = 3749 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3371 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9109252E-10 -3.8938786E-10 midg,1,midg; midg,igrid,midg -2.4434599E-09 1.5805219E-09 1,midg,midg; igrid,midg,midg -2.9993566E-10 4.5797990E-10 gauss-seidel spectral radius is 0.9835026 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 16:52:47 rms-change max change #iterations 9.2380799E-02 14.14655 at 10iterations 6.4785238E-03 1.021650 at 20iterations 4.6478107E-04 6.6263199E-02 at 30iterations 4.4084041E-05 6.7558289E-03 at 40iterations 1.3627389E-05 1.9273758E-03 at 50iterations finished qdiffx linear iterations at : 16:52:50 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.3627389E-05 1.9273758E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 16:52:50 4.215u 0.228s 0:04.72 93.8% 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 Sat Oct 8 2011 at 16:52:50 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3579 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: 1.674847 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 1.674847 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 545.7455 centred at (gu) : 94.23802 87.88898 84.53921 assigned negative charge : -546.2469 centred at (gu) : 94.15057 87.42573 84.67006 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33098 grid for indexing accessible points = 1.400000 m= 25270 mr = 54564 m= 3047 mr = 16862 m= 115 mr = 1573 m= 0 mr = 19 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 36641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 26660 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) : 0.5582825 object centre at (A) : 47.35650 155.9215 29.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2093688E-03 9.8819342E-03 midg,1,midg; midg,igrid,midg -1.8689668E-02 2.0787068E-02 1,midg,midg; igrid,midg,midg -1.1344207E-02 -2.0557435E-02 gauss-seidel spectral radius is 0.9983550 estimated iterations to convergence 196 setup time was (sec) 0.9200000 now iterating at: 16:52:52 rms-change max change #iterations 3.942847 156.4918 at 10iterations 1.717944 56.72822 at 20iterations 0.7461593 25.52103 at 30iterations 0.3240694 11.46695 at 40iterations 0.1413055 4.893678 at 50iterations 6.1585035E-02 1.940529 at 60iterations 2.6806742E-02 0.9641800 at 70iterations 1.1710447E-02 0.3856735 at 80iterations 5.1074363E-03 0.1722558 at 90iterations 2.2340266E-03 6.7139149E-02 at 100iterations 9.8492950E-04 3.4618378E-02 at 110iterations 4.4488232E-04 1.6026497E-02 at 120iterations finished qdiffx linear iterations at : 16:53:00 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 4.4488232E-04 1.6026497E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 16:53:01 9.538u 0.265s 0:10.06 97.3% 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 Sat Oct 8 2011 at 16:53:01 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3579 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: 2.512271 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): 15.47300 79.24000 ymin,ymax (A): 128.0700 183.7730 zmin,zma (A): -1.286000 60.04300 x,y,z range (A): 63.76700 55.70299 61.32900 scale (grids/A): 2.512271 object centre (A): 47.35650 155.9215 29.37850 number of atom coordinates read : 3579 total number of charged atoms : 3457 net assigned charge : -0.4999836 assigned positive charge : 545.7455 centred at (gu) : 96.35679 86.83330 81.80861 assigned negative charge : -546.2469 centred at (gu) : 96.22585 86.13863 82.00497 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 188416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33098 grid for indexing accessible points = 1.400000 m= 86496 mr = 133732 m= 25592 mr = 67168 m= 4907 mr = 18830 m= 454 mr = 3275 m= 11 mr = 243 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 82628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 27644 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) : 1.674847 object centre at (A) : 47.35650 155.9215 29.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2179193 0.2640574 midg,1,midg; midg,igrid,midg -0.2725905 0.3247204 1,midg,midg; igrid,midg,midg -0.1946265 -0.3804770 gauss-seidel spectral radius is 0.9992144 estimated iterations to convergence 282 setup time was (sec) 1.840000 now iterating at: 16:53:03 rms-change max change #iterations 10.18488 302.5527 at 10iterations 5.938837 139.7647 at 20iterations 3.444662 73.21605 at 30iterations 1.986931 41.10920 at 40iterations 1.139914 22.47551 at 50iterations 0.6514862 12.54172 at 60iterations 0.3719745 7.378428 at 70iterations 0.2118300 4.062747 at 80iterations 0.1202868 2.302002 at 90iterations 6.8273380E-02 1.513475 at 100iterations 3.8783014E-02 0.7412295 at 110iterations 2.1988165E-02 0.3902502 at 120iterations 1.2439297E-02 0.2241209 at 130iterations 7.0695989E-03 0.1338425 at 140iterations 3.9904830E-03 7.5117111E-02 at 150iterations 2.2604095E-03 3.8913727E-02 at 160iterations 1.2788500E-03 2.3462415E-02 at 170iterations 7.2270416E-04 1.2169838E-02 at 180iterations finished qdiffx linear iterations at : 16:53:16 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 7.2270416E-04 1.2169838E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 16:53:17 15.423u 0.256s 0:15.96 98.1% 0+0k 0+0io 0pf+0w