Mon Oct 10 17:03:42 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+sph.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 = amb.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 17:03:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4787 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5123482 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): -18.82600 37.00100 ymin,ymax (A): -30.56000 34.61100 zmin,zma (A): -4.169000 65.31500 x,y,z range (A): 55.82700 65.17100 69.48400 scale (grids/A): 0.5123482 object centre (A): 9.087502 2.025500 30.57300 number of atom coordinates read : 4787 total number of charged atoms : 4541 net assigned charge : 3.800025 assigned positive charge : 718.1924 centred at (gu) : 90.31639 90.43482 88.32507 assigned negative charge : -714.3969 centred at (gu) : 90.19495 90.46149 88.33373 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7951 nv = 96 ne = 84 npr = 97405 no. pairs analyzed = 97405 no. exposed pairs = 6068 no. arc points = 41831 no. surface atoms = 2013 nbur = 2774 mkacc time = 0.2700000 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 = 1.652000 m= 284 mr = 4110 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3982 ## 549 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 10491 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2556652E-10 2.1798612E-11 midg,1,midg; midg,igrid,midg 1.1696705E-10 -2.0115675E-11 1,midg,midg; igrid,midg,midg -2.6352096E-10 4.2405951E-10 gauss-seidel spectral radius is 0.9805179 estimated iterations to convergence 59 setup time was (sec) 0.8200000 now iterating at: 17:03:43 rms-change max change #iterations 6.8650268E-02 11.48063 at 10iterations 4.0430464E-03 0.6725998 at 20iterations 3.6216743E-04 5.7647705E-02 at 30iterations 1.0759381E-04 1.9457102E-02 at 40iterations 4.2307136E-05 7.8678131E-03 at 50iterations finished qdiffx linear iterations at : 17:03:47 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 4.2307136E-05 7.8678131E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 17:03:48 4.315u 0.275s 0:05.69 80.4% 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 17:03:48 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4787 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.537045 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): -18.82600 37.00100 ymin,ymax (A): -30.56000 34.61100 zmin,zma (A): -4.169000 65.31500 x,y,z range (A): 55.82700 65.17100 69.48400 scale (grids/A): 1.537045 object centre (A): 9.087502 2.025500 30.57300 number of atom coordinates read : 4787 total number of charged atoms : 4541 net assigned charge : 3.800025 assigned positive charge : 718.1924 centred at (gu) : 90.94796 91.30322 84.97369 assigned negative charge : -714.3969 centred at (gu) : 90.58470 91.38438 85.00086 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 89933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25530 mr = 61928 m= 2212 mr = 16659 m= 46 mr = 896 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.8000000 number of dielectric boundary points 38239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 34230 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) : 0.5123482 object centre at (A) : 9.087502 2.025500 30.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8824484E-03 1.6383680E-02 midg,1,midg; midg,igrid,midg -1.8597747E-03 -1.1984247E-02 1,midg,midg; igrid,midg,midg -2.0576811E-03 1.2080956E-02 gauss-seidel spectral radius is 0.9981263 estimated iterations to convergence 184 setup time was (sec) 1.120000 now iterating at: 17:03:49 rms-change max change #iterations 3.813854 153.4124 at 10iterations 1.568632 58.83646 at 20iterations 0.6446827 22.57569 at 30iterations 0.2656246 9.141102 at 40iterations 0.1091800 3.240105 at 50iterations 4.5026049E-02 1.340996 at 60iterations 1.8536327E-02 0.5836535 at 70iterations 7.6581370E-03 0.2440052 at 80iterations 3.1681743E-03 9.7263932E-02 at 90iterations 1.3014916E-03 3.9592743E-02 at 100iterations 5.4004643E-04 1.7196655E-02 at 110iterations 2.2337255E-04 7.5225830E-03 at 120iterations finished qdiffx linear iterations at : 17:03:58 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 2.2337255E-04 7.5225830E-03 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 17:04:00 9.842u 0.305s 0:11.77 86.1% 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 17:04:00 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4787 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.305567 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): -18.82600 37.00100 ymin,ymax (A): -30.56000 34.61100 zmin,zma (A): -4.169000 65.31500 x,y,z range (A): 55.82700 65.17100 69.48400 scale (grids/A): 2.305567 object centre (A): 9.087502 2.025500 30.57300 number of atom coordinates read : 4787 total number of charged atoms : 4541 net assigned charge : 3.800025 assigned positive charge : 718.1924 centred at (gu) : 91.42159 91.95448 82.46004 assigned negative charge : -714.3969 centred at (gu) : 90.87695 92.07651 82.50117 start vw surface at 0.2200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 209953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92121 mr = 152438 m= 22519 mr = 71579 m= 3106 mr = 15839 m= 139 mr = 1801 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 291 time to turn everything in is 1.950000 number of dielectric boundary points 86133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 36216 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) : 1.537045 object centre at (A) : 9.087502 2.025500 30.57300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1300907 0.4438148 midg,1,midg; midg,igrid,midg -0.1549788 -0.2963066 1,midg,midg; igrid,midg,midg -2.1139544E-02 0.1830977 gauss-seidel spectral radius is 0.9991673 estimated iterations to convergence 274 setup time was (sec) 2.270000 now iterating at: 17:04:02 rms-change max change #iterations 10.30793 285.0002 at 10iterations 5.928055 145.9748 at 20iterations 3.377927 87.28818 at 30iterations 1.912034 49.10709 at 40iterations 1.081183 23.30030 at 50iterations 0.6084514 12.23740 at 60iterations 0.3413502 7.537607 at 70iterations 0.1912984 3.838503 at 80iterations 0.1071468 2.002713 at 90iterations 5.9802145E-02 1.179927 at 100iterations 3.3311378E-02 0.6854401 at 110iterations 1.8596403E-02 0.3895149 at 120iterations 1.0387992E-02 0.2075000 at 130iterations 5.7827923E-03 0.1143341 at 140iterations 3.2224380E-03 6.2060475E-02 at 150iterations 1.7940638E-03 3.6987305E-02 at 160iterations 1.0023068E-03 1.9602776E-02 at 170iterations 5.6026079E-04 1.1528015E-02 at 180iterations finished qdiffx linear iterations at : 17:04:17 total time elapsed so far: 16.50000 # loops : 180 mean,max change (kT/e) : 5.6026079E-04 1.1528015E-02 energy calculations done at 16.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 17:04:17 16.687u 0.345s 0:17.78 95.7% 0+0k 0+0io 0pf+0w