Sat Oct 15 13:25:59 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 15 2011 at 13:25:59 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7306911 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 0.7306911 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.4250 centred at (gu) : 91.90157 91.50795 91.49888 assigned negative charge : -144.9250 centred at (gu) : 91.71761 91.62363 91.19498 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4062 nv = 96 ne = 84 npr = 20221 no. pairs analyzed = 20221 no. exposed pairs = 1635 no. arc points = 12155 no. surface atoms = 551 nbur = 493 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 1824 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1100000 number of dielectric boundary points 2492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 961 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 3943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3851773E-08 1.7409731E-07 midg,1,midg; midg,igrid,midg 4.6777778E-08 -3.4234635E-08 1,midg,midg; igrid,midg,midg -3.5457251E-08 1.2583227E-07 gauss-seidel spectral radius is 0.9901441 estimated iterations to convergence 82 setup time was (sec) 0.3300000 now iterating at: 13:25:59 rms-change max change #iterations 0.1557572 28.32518 at 10iterations 2.0225134E-02 4.717295 at 20iterations 2.5703539E-03 0.4498901 at 30iterations 3.3244639E-04 6.2158585E-02 at 40iterations 4.2515843E-05 8.2149506E-03 at 50iterations finished qdiffx linear iterations at : 13:26:03 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 4.2515843E-05 8.2149506E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 13:26:03 3.756u 0.226s 0:04.33 91.6% 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 15 2011 at 13:26:03 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.192073 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 2.192073 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.4250 centred at (gu) : 95.70477 94.52389 94.49666 assigned negative charge : -144.9250 centred at (gu) : 95.15290 94.87103 93.58499 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 40845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12155 grid for indexing accessible points = 1.400000 m= 15691 mr = 24138 m= 3787 mr = 11083 m= 450 mr = 2521 m= 16 mr = 208 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 22836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 7311 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) : 0.7306911 object centre at (A) : -8.966999 21.99700 35.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9161599E-04 4.4116575E-02 midg,1,midg; midg,igrid,midg 1.9564645E-02 7.5937407E-03 1,midg,midg; igrid,midg,midg -8.2370257E-03 3.2593221E-03 gauss-seidel spectral radius is 0.9988090 estimated iterations to convergence 229 setup time was (sec) 0.5000000 now iterating at: 13:26:04 rms-change max change #iterations 3.279427 166.2529 at 10iterations 1.592979 84.34330 at 20iterations 0.7785821 38.37334 at 30iterations 0.3807738 16.12385 at 40iterations 0.1868591 7.410289 at 50iterations 9.1401272E-02 3.513535 at 60iterations 4.4714652E-02 1.983122 at 70iterations 2.1857267E-02 0.8858553 at 80iterations 1.0716270E-02 0.4137740 at 90iterations 5.2297553E-03 0.2203252 at 100iterations 2.5702436E-03 9.6616745E-02 at 110iterations 1.2590584E-03 5.3073227E-02 at 120iterations finished qdiffx linear iterations at : 13:26:12 total time elapsed so far: 8.550000 # loops : 120 mean,max change (kT/e) : 1.2590584E-03 5.3073227E-02 energy calculations done at 8.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.690000 DelPhi exited at 13:26:12 8.692u 0.280s 0:09.33 96.1% 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 Sat Oct 15 2011 at 13:26:13 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 3.288110 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): -28.66400 10.73000 ymin,ymax (A): 1.353000 42.64100 zmin,zma (A): 11.08300 59.80400 x,y,z range (A): 39.39400 41.28800 48.72100 scale (grids/A): 3.288110 object centre (A): -8.966999 21.99700 35.44350 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.4250 centred at (gu) : 98.55721 96.78584 96.74492 assigned negative charge : -144.9250 centred at (gu) : 97.72936 97.30650 95.37756 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12155 grid for indexing accessible points = 1.400000 m= 46278 mr = 58758 m= 21313 mr = 36060 m= 7383 mr = 17135 m= 1689 mr = 5687 m= 193 mr = 1135 m= 10 mr = 86 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 51409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 7344 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) : 2.192073 object centre at (A) : -8.966999 21.99700 35.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8696902E-02 0.3084524 midg,1,midg; midg,igrid,midg 0.1489518 6.6009849E-02 1,midg,midg; igrid,midg,midg -2.7794497E-02 -9.5106093E-03 gauss-seidel spectral radius is 0.9992942 estimated iterations to convergence 297 setup time was (sec) 0.9800000 now iterating at: 13:26:14 rms-change max change #iterations 7.367373 316.7308 at 10iterations 4.362669 167.9890 at 20iterations 2.570966 70.94714 at 30iterations 1.511007 40.80905 at 40iterations 0.8849727 25.22362 at 50iterations 0.5159746 12.51423 at 60iterations 0.3004790 7.431768 at 70iterations 0.1750558 4.100968 at 80iterations 0.1018904 2.588545 at 90iterations 5.9105154E-02 1.573754 at 100iterations 3.4426454E-02 0.8368664 at 110iterations 1.9978110E-02 0.4353352 at 120iterations 1.1613001E-02 0.2794094 at 130iterations 6.7444439E-03 0.1708641 at 140iterations 3.9047832E-03 8.3572388E-02 at 150iterations 2.2744688E-03 4.9915314E-02 at 160iterations 1.3144172E-03 3.0073166E-02 at 170iterations 7.6210260E-04 1.7229080E-02 at 180iterations finished qdiffx linear iterations at : 13:26:27 total time elapsed so far: 13.75000 # loops : 180 mean,max change (kT/e) : 7.6210260E-04 1.7229080E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 13:26:27 13.888u 0.304s 0:14.76 96.0% 0+0k 0+0io 0pf+0w