Mon Oct 10 17:06:29 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 17:06:29 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 826 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5115604 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): -16.66800 37.15200 ymin,ymax (A): -32.99900 31.33700 zmin,zma (A): -4.009000 65.58200 x,y,z range (A): 53.82000 64.33600 69.59100 scale (grids/A): 0.5115604 object centre (A): 10.24200 -0.8310003 30.78650 number of atom coordinates read : 4328 total number of charged atoms : 4080 net assigned charge : 3.206026 assigned positive charge : 644.4783 centred at (gu) : 90.24588 91.01397 87.54540 assigned negative charge : -641.2762 centred at (gu) : 90.11306 91.04793 87.59051 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7217 nv = 96 ne = 84 npr = 87795 no. pairs analyzed = 87795 no. exposed pairs = 5605 no. arc points = 39060 no. surface atoms = 1879 nbur = 2449 mkacc time = 0.1900000 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= 260 mr = 3632 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3757 ## 572 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9336703E-10 -3.3239529E-11 midg,1,midg; midg,igrid,midg 9.6400089E-11 -5.0248711E-11 1,midg,midg; igrid,midg,midg -2.6280880E-10 3.8229814E-10 gauss-seidel spectral radius is 0.9804280 estimated iterations to convergence 59 setup time was (sec) 0.6200000 now iterating at: 17:06:30 rms-change max change #iterations 6.3272566E-02 10.91762 at 10iterations 3.6485093E-03 0.6229448 at 20iterations 2.6271516E-04 3.6935806E-02 at 30iterations 6.0671980E-05 9.1381073E-03 at 40iterations 2.2143147E-05 3.4844875E-03 at 50iterations finished qdiffx linear iterations at : 17:06:33 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 2.2143147E-05 3.4844875E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 17:06:33 3.279u 0.204s 0:03.81 91.0% 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 17:06:33 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 826 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.534681 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): -16.66800 37.15200 ymin,ymax (A): -32.99900 31.33700 zmin,zma (A): -4.009000 65.58200 x,y,z range (A): 53.82000 64.33600 69.59100 scale (grids/A): 1.534681 object centre (A): 10.24200 -0.8310003 30.78650 number of atom coordinates read : 4328 total number of charged atoms : 4080 net assigned charge : 3.206026 assigned positive charge : 644.4783 centred at (gu) : 90.73660 93.04044 82.63494 assigned negative charge : -641.2762 centred at (gu) : 90.33917 93.14361 82.77135 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22854 mr = 55505 m= 1923 mr = 14686 m= 45 mr = 751 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.5600000 number of dielectric boundary points 35391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 30677 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) : 0.5115604 object centre at (A) : 10.24200 -0.8310003 30.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7594821E-03 7.5333659E-03 midg,1,midg; midg,igrid,midg 4.8997499E-05 -8.5457694E-03 1,midg,midg; igrid,midg,midg -3.6752988E-03 1.0709427E-02 gauss-seidel spectral radius is 0.9980802 estimated iterations to convergence 181 setup time was (sec) 0.8100000 now iterating at: 17:06:34 rms-change max change #iterations 3.580246 167.5669 at 10iterations 1.446189 54.15695 at 20iterations 0.5880146 19.82546 at 30iterations 0.2390597 8.095672 at 40iterations 9.7017378E-02 3.870530 at 50iterations 3.9697710E-02 1.281984 at 60iterations 1.6151926E-02 0.5497246 at 70iterations 6.5638185E-03 0.2207718 at 80iterations 2.6879704E-03 0.1044807 at 90iterations 1.0954217E-03 4.0563583E-02 at 100iterations 4.4687523E-04 1.4189243E-02 at 110iterations 1.8322140E-04 6.5374374E-03 at 120iterations finished qdiffx linear iterations at : 17:06:40 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.8322140E-04 6.5374374E-03 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 17:06:41 6.958u 0.188s 0:07.54 94.5% 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 17:06:41 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4328 !!! WARNING: GLM 172 has a net charge of -0.0940 !!! WARNING: HEM 826 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: 2.302022 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): -16.66800 37.15200 ymin,ymax (A): -32.99900 31.33700 zmin,zma (A): -4.009000 65.58200 x,y,z range (A): 53.82000 64.33600 69.59100 scale (grids/A): 2.302022 object centre (A): 10.24200 -0.8310003 30.78650 number of atom coordinates read : 4328 total number of charged atoms : 4080 net assigned charge : 3.206026 assigned positive charge : 644.4783 centred at (gu) : 91.10453 94.56063 78.95200 assigned negative charge : -641.2762 centred at (gu) : 90.50868 94.71541 79.15712 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 190355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 83292 mr = 136672 m= 19859 mr = 64159 m= 2578 mr = 13860 m= 145 mr = 1449 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 1.310000 number of dielectric boundary points 80041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 32567 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) : 1.534681 object centre at (A) : 10.24200 -0.8310003 30.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2331479 0.2326213 midg,1,midg; midg,igrid,midg -9.0083376E-02 -0.2562702 1,midg,midg; igrid,midg,midg -4.4058714E-02 0.1660663 gauss-seidel spectral radius is 0.9991432 estimated iterations to convergence 270 setup time was (sec) 1.610000 now iterating at: 17:06:43 rms-change max change #iterations 9.741319 282.1125 at 10iterations 5.550461 140.2039 at 20iterations 3.133037 76.32980 at 30iterations 1.763104 42.50665 at 40iterations 0.9885060 23.44188 at 50iterations 0.5511293 12.04937 at 60iterations 0.3061943 6.041880 at 70iterations 0.1698284 3.308278 at 80iterations 9.4463393E-02 1.969508 at 90iterations 5.2325666E-02 1.126901 at 100iterations 2.8936421E-02 0.5891609 at 110iterations 1.6045453E-02 0.3223190 at 120iterations 8.8408841E-03 0.2133312 at 130iterations 4.8860968E-03 0.1007690 at 140iterations 2.6955078E-03 5.6760788E-02 at 150iterations 1.4918746E-03 3.0204773E-02 at 160iterations 8.2463608E-04 1.5815735E-02 at 170iterations 4.5688092E-04 9.0246201E-03 at 180iterations finished qdiffx linear iterations at : 17:06:53 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 4.5688092E-04 9.0246201E-03 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 17:06:53 11.727u 0.194s 0:12.57 94.7% 0+0k 0+0io 0pf+0w