Sat Oct 8 11:47:57 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 11:47:57 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5559 !!! WARNING: GLM 244 has a net charge of -0.0940 !!! WARNING: HIR 316 has a net charge of 0.5140 !!! WARNING: HIR 346 has a net charge of 0.5140 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 373 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.5316607 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 0.5316607 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5383 net assigned charge : 1.476031 assigned positive charge : 851.1713 centred at (gu) : 89.68557 90.60327 90.46545 assigned negative charge : -849.7014 centred at (gu) : 89.70658 90.60471 90.49784 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 9658 nv = 96 ne = 84 npr = 115871 no. pairs analyzed = 115871 no. exposed pairs = 6494 no. arc points = 43960 no. surface atoms = 2174 nbur = 3385 mkacc time = 0.3200000 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 = 1.624000 m= 363 mr = 5341 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3500001 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.6600000 number of dielectric boundary points 4671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4422 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 13120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5636374E-10 -2.1018393E-10 midg,1,midg; midg,igrid,midg 5.4171747E-11 4.8376619E-11 1,midg,midg; igrid,midg,midg 2.2311655E-10 -9.3985653E-11 gauss-seidel spectral radius is 0.9819444 estimated iterations to convergence 61 setup time was (sec) 0.9400000 now iterating at: 11:47:58 rms-change max change #iterations 9.1369353E-02 12.93951 at 10iterations 7.3405388E-03 1.348579 at 20iterations 1.2354725E-03 0.3018494 at 30iterations 3.4437998E-04 7.2494507E-02 at 40iterations 1.3085025E-04 1.7387390E-02 at 50iterations finished qdiffx linear iterations at : 11:48:01 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.3085025E-04 1.7387390E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 11:48:02 4.309u 0.165s 0:04.75 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 11:48:02 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5559 !!! WARNING: GLM 244 has a net charge of -0.0940 !!! WARNING: HIR 316 has a net charge of 0.5140 !!! WARNING: HIR 346 has a net charge of 0.5140 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 373 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.594982 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 1.594982 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5383 net assigned charge : 1.476031 assigned positive charge : 851.1713 centred at (gu) : 89.05493 91.80836 91.39447 assigned negative charge : -849.7014 centred at (gu) : 89.11946 91.81385 91.49329 start vw surface at 0.2800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 109426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43960 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33452 mr = 78035 m= 3231 mr = 23222 m= 93 mr = 1567 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1792 time to turn everything in is 0.9500000 number of dielectric boundary points 43377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 591 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 40976 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) : 0.5316607 object centre at (A) : 47.31450 43.69750 42.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4498442E-02 1.5874177E-02 midg,1,midg; midg,igrid,midg 1.4160244E-02 -5.7434961E-03 1,midg,midg; igrid,midg,midg 1.4798447E-03 -6.2700901E-03 gauss-seidel spectral radius is 0.9983295 estimated iterations to convergence 194 setup time was (sec) 1.300000 now iterating at: 11:48:03 rms-change max change #iterations 4.601223 217.3163 at 10iterations 1.986649 63.65647 at 20iterations 0.8582880 26.79000 at 30iterations 0.3718672 10.39277 at 40iterations 0.1611965 5.427483 at 50iterations 6.9955118E-02 2.001021 at 60iterations 3.0428601E-02 0.9101486 at 70iterations 1.3307887E-02 0.3722916 at 80iterations 5.8765300E-03 0.1659012 at 90iterations 2.6229904E-03 7.5950623E-02 at 100iterations 1.2131508E-03 3.9054871E-02 at 110iterations 6.0271984E-04 1.9912720E-02 at 120iterations finished qdiffx linear iterations at : 11:48:11 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 6.0271984E-04 1.9912720E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 11:48:12 9.324u 0.185s 0:10.03 94.7% 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 11:48:12 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5559 !!! WARNING: GLM 244 has a net charge of -0.0940 !!! WARNING: HIR 316 has a net charge of 0.5140 !!! WARNING: HIR 346 has a net charge of 0.5140 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 373 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.392473 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): 16.00200 78.62700 ymin,ymax (A): 10.96900 76.42600 zmin,zma (A): 8.542000 75.50200 x,y,z range (A): 62.62500 65.45700 66.96000 scale (grids/A): 2.392473 object centre (A): 47.31450 43.69750 42.02200 number of atom coordinates read : 5559 total number of charged atoms : 5383 net assigned charge : 1.476031 assigned positive charge : 851.1713 centred at (gu) : 88.58176 92.71227 92.09129 assigned negative charge : -849.7014 centred at (gu) : 88.67896 92.72062 92.24002 start vw surface at 0.2800000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 255698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43960 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 117110 mr = 191324 m= 32577 mr = 93469 m= 5029 mr = 24464 m= 310 mr = 3277 m= 4 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 6320 time to turn everything in is 2.360000 number of dielectric boundary points 98057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 42988 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) : 1.594982 object centre at (A) : 47.31450 43.69750 42.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4217616 0.2159856 midg,1,midg; midg,igrid,midg 0.1926883 -0.1658833 1,midg,midg; igrid,midg,midg 8.5198276E-02 -0.1253065 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 2.730000 now iterating at: 11:48:15 rms-change max change #iterations 12.05832 301.1115 at 10iterations 7.103520 169.4834 at 20iterations 4.161504 87.01283 at 30iterations 2.431523 55.70779 at 40iterations 1.410754 29.25578 at 50iterations 0.8188342 16.90942 at 60iterations 0.4721770 8.463524 at 70iterations 0.2726577 6.256212 at 80iterations 0.1574067 2.968189 at 90iterations 9.0607740E-02 1.597563 at 100iterations 5.2038856E-02 0.9897232 at 110iterations 2.9926801E-02 0.5745773 at 120iterations 1.7198807E-02 0.3350601 at 130iterations 9.9025154E-03 0.1792507 at 140iterations 5.6953956E-03 0.1085434 at 150iterations 3.2970202E-03 5.9997082E-02 at 160iterations 1.9225038E-03 3.4698486E-02 at 170iterations 1.1314487E-03 2.1898270E-02 at 180iterations finished qdiffx linear iterations at : 11:48:27 total time elapsed so far: 15.16000 # loops : 180 mean,max change (kT/e) : 1.1314487E-03 2.1898270E-02 energy calculations done at 15.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 11:48:28 15.402u 0.182s 0:15.85 98.2% 0+0k 0+0io 0pf+0w