Mon Oct 10 14:03:16 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 14:03:16 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 = 2815 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5443592 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 0.5443592 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.014022 assigned positive charge : 409.2499 centred at (gu) : 88.70861 89.57367 87.25223 assigned negative charge : -401.2364 centred at (gu) : 88.55339 89.51865 87.08136 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5633 nv = 96 ne = 84 npr = 53994 no. pairs analyzed = 53994 no. exposed pairs = 4211 no. arc points = 30677 no. surface atoms = 1393 nbur = 1422 mkacc time = 0.1500000 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 = 1.568000 m= 255 mr = 2487 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2984 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7238 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7109221E-10 7.3484691E-10 midg,1,midg; midg,igrid,midg 2.1975023E-10 7.3129391E-10 1,midg,midg; igrid,midg,midg -5.2818028E-10 9.8566288E-10 gauss-seidel spectral radius is 0.9826078 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 14:03:17 rms-change max change #iterations 6.9462135E-02 11.81252 at 10iterations 4.5529907E-03 0.7796969 at 20iterations 3.1045405E-04 5.1170349E-02 at 30iterations 3.1818727E-05 4.6596527E-03 at 40iterations 6.1673240E-06 8.2095712E-04 at 50iterations finished qdiffx linear iterations at : 14:03:22 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 6.1673240E-06 8.2095712E-04 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.490000 DelPhi exited at 14:03:23 5.498u 0.461s 0:07.01 84.8% 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 14:03:23 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 = 2815 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.633078 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 1.633078 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.014022 assigned positive charge : 409.2499 centred at (gu) : 86.12518 88.72060 81.75606 assigned negative charge : -401.2364 centred at (gu) : 85.65984 88.55591 81.24364 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18526 mr = 37234 m= 1969 mr = 11755 m= 60 mr = 802 m= 0 mr = 4 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 0.6000000 number of dielectric boundary points 31590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20444 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) : 0.5443592 object centre at (A) : -10.94000 138.4675 182.1510 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4334442E-03 8.5971765E-03 midg,1,midg; midg,igrid,midg 1.1319500E-02 1.7369919E-02 1,midg,midg; igrid,midg,midg -2.0980775E-02 1.8249059E-02 gauss-seidel spectral radius is 0.9981872 estimated iterations to convergence 187 setup time was (sec) 0.9800000 now iterating at: 14:03:25 rms-change max change #iterations 3.140921 168.1053 at 10iterations 1.301776 64.55579 at 20iterations 0.5395725 19.97214 at 30iterations 0.2241310 8.528483 at 40iterations 9.3068272E-02 3.481393 at 50iterations 3.8815275E-02 1.423509 at 60iterations 1.6114241E-02 0.6036944 at 70iterations 6.7075235E-03 0.2507554 at 80iterations 2.7852093E-03 0.1048868 at 90iterations 1.1679298E-03 4.2881012E-02 at 100iterations 4.8687542E-04 1.8606663E-02 at 110iterations 2.0410634E-04 7.7123642E-03 at 120iterations finished qdiffx linear iterations at : 14:03:36 total time elapsed so far: 12.73000 # loops : 120 mean,max change (kT/e) : 2.0410634E-04 7.7123642E-03 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 14:03:37 12.921u 0.469s 0:14.18 94.3% 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 Mon Oct 10 2011 at 14:03:38 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 = 2815 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.449616 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): -43.63900 21.75900 ymin,ymax (A): 110.8280 166.1070 zmin,zma (A): 155.8160 208.4860 x,y,z range (A): 65.39799 55.27900 52.67001 scale (grids/A): 2.449616 object centre (A): -10.94000 138.4675 182.1510 number of atom coordinates read : 2815 total number of charged atoms : 2665 net assigned charge : 8.014022 assigned positive charge : 409.2499 centred at (gu) : 84.18758 88.08052 77.63409 assigned negative charge : -401.2364 centred at (gu) : 83.48967 87.83385 76.86537 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 140702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62479 mr = 92086 m= 18414 mr = 46555 m= 2897 mr = 12993 m= 184 mr = 1617 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1331 time to turn everything in is 1.500000 number of dielectric boundary points 71355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 21304 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) : 1.633078 object centre at (A) : -10.94000 138.4675 182.1510 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7382777E-02 0.1113136 midg,1,midg; midg,igrid,midg 0.1655536 0.3662045 1,midg,midg; igrid,midg,midg -0.6298042 0.7027005 gauss-seidel spectral radius is 0.9991434 estimated iterations to convergence 270 setup time was (sec) 1.950000 now iterating at: 14:03:40 rms-change max change #iterations 8.424388 308.9933 at 10iterations 4.830620 139.6563 at 20iterations 2.740345 90.98912 at 30iterations 1.541000 47.68517 at 40iterations 0.8609095 24.78447 at 50iterations 0.4804372 13.35599 at 60iterations 0.2672396 6.921969 at 70iterations 0.1485463 4.415611 at 80iterations 8.2232870E-02 2.048058 at 90iterations 4.5500614E-02 1.177834 at 100iterations 2.5129681E-02 0.6459253 at 110iterations 1.3853996E-02 0.3015099 at 120iterations 7.6412773E-03 0.1888580 at 130iterations 4.2305905E-03 9.8464966E-02 at 140iterations 2.3246065E-03 5.4321289E-02 at 150iterations 1.2832318E-03 2.7999878E-02 at 160iterations 7.0715981E-04 1.5338898E-02 at 170iterations 3.8954595E-04 9.0770721E-03 at 180iterations finished qdiffx linear iterations at : 14:03:59 total time elapsed so far: 20.46000 # loops : 180 mean,max change (kT/e) : 3.8954595E-04 9.0770721E-03 energy calculations done at 20.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.65000 DelPhi exited at 14:04:00 20.647u 0.521s 0:21.92 96.5% 0+0k 0+0io 0pf+0w