Sat Oct 8 13:45:43 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 Sat Oct 8 2011 at 13:45:43 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6397240 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 0.6397240 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0455 centred at (gu) : 89.13164 89.55049 91.63815 assigned negative charge : -454.0463 centred at (gu) : 89.12590 89.46143 91.54884 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8170 nv = 96 ne = 84 npr = 63443 no. pairs analyzed = 63443 no. exposed pairs = 3478 no. arc points = 24091 no. surface atoms = 1186 nbur = 1845 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4749 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2394 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10052 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6409218E-09 1.6927695E-08 midg,1,midg; midg,igrid,midg -1.3553329E-08 1.0666478E-08 1,midg,midg; igrid,midg,midg -1.1101945E-09 5.2278726E-10 gauss-seidel spectral radius is 0.9873717 estimated iterations to convergence 73 setup time was (sec) 0.6800000 now iterating at: 13:45:44 rms-change max change #iterations 0.1585848 23.97442 at 10iterations 1.6443918E-02 2.041405 at 20iterations 1.6746412E-03 0.2456551 at 30iterations 1.8626984E-04 2.5909424E-02 at 40iterations 2.5165853E-05 3.0632019E-03 at 50iterations finished qdiffx linear iterations at : 13:45:47 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 2.5165853E-05 3.0632019E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 13:45:47 4.196u 0.261s 0:04.76 93.4% 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 Sat Oct 8 2011 at 13:45:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.919172 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 1.919172 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0455 centred at (gu) : 87.39405 88.65098 94.91403 assigned negative charge : -454.0463 centred at (gu) : 87.37759 88.38390 94.64629 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 89653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24091 grid for indexing accessible points = 1.400000 m= 32577 mr = 64857 m= 4924 mr = 24488 m= 322 mr = 3054 m= 4 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.7600000 number of dielectric boundary points 34961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22733 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) : 0.6397240 object centre at (A) : 15.20400 0.1504993 20.10650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7792067E-02 2.2031641E-02 midg,1,midg; midg,igrid,midg -3.1215020E-03 2.4352264E-02 1,midg,midg; igrid,midg,midg -3.0286074E-02 6.9591347E-03 gauss-seidel spectral radius is 0.9986903 estimated iterations to convergence 219 setup time was (sec) 1.070000 now iterating at: 13:45:49 rms-change max change #iterations 4.714457 186.2908 at 10iterations 2.254173 79.56467 at 20iterations 1.070833 30.67820 at 30iterations 0.5105867 14.98805 at 40iterations 0.2436185 7.088478 at 50iterations 0.1161178 3.286478 at 60iterations 5.5198442E-02 1.545413 at 70iterations 2.6395515E-02 0.7363281 at 80iterations 1.2557932E-02 0.3660564 at 90iterations 6.0167410E-03 0.1610966 at 100iterations 2.8613538E-03 8.0944061E-02 at 110iterations 1.3713473E-03 3.9924622E-02 at 120iterations finished qdiffx linear iterations at : 13:45:57 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 1.3713473E-03 3.9924622E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 13:45:58 9.746u 0.333s 0:10.38 97.0% 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 Sat Oct 8 2011 at 13:45:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.878758 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): -11.97200 42.38000 ymin,ymax (A): -22.68000 22.98100 zmin,zma (A): -7.718000 47.93100 x,y,z range (A): 54.35200 45.66100 55.64900 scale (grids/A): 2.878758 object centre (A): 15.20400 0.1504993 20.10650 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0455 centred at (gu) : 86.09087 87.97644 97.37096 assigned negative charge : -454.0463 centred at (gu) : 86.06629 87.57568 96.96938 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 207738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24091 grid for indexing accessible points = 1.400000 m= 106947 mr = 156508 m= 37364 mr = 89072 m= 8654 mr = 30382 m= 1304 mr = 6412 m= 83 mr = 888 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 753 time to turn everything in is 2.030000 number of dielectric boundary points 78797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 23072 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) : 1.919172 object centre at (A) : 15.20400 0.1504993 20.10650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9311453E-02 0.3058084 midg,1,midg; midg,igrid,midg -3.0248808E-02 0.3178745 1,midg,midg; igrid,midg,midg -0.4838248 0.1355617 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 2.360000 now iterating at: 13:46:01 rms-change max change #iterations 10.91294 427.6051 at 10iterations 6.406510 131.8695 at 20iterations 3.731030 78.87720 at 30iterations 2.177734 39.01901 at 40iterations 1.262431 22.16693 at 50iterations 0.7334964 12.38091 at 60iterations 0.4261536 7.661449 at 70iterations 0.2474286 4.595684 at 80iterations 0.1431906 2.332980 at 90iterations 8.2874097E-02 1.365726 at 100iterations 4.7993757E-02 0.7384720 at 110iterations 2.7766256E-02 0.4471829 at 120iterations 1.6090544E-02 0.2480679 at 130iterations 9.3419300E-03 0.1478043 at 140iterations 5.4094750E-03 8.7456226E-02 at 150iterations 3.1481688E-03 5.1961899E-02 at 160iterations 1.8333152E-03 3.1982422E-02 at 170iterations 1.0748841E-03 1.8392563E-02 at 180iterations finished qdiffx linear iterations at : 13:46:15 total time elapsed so far: 16.49000 # loops : 180 mean,max change (kT/e) : 1.0748841E-03 1.8392563E-02 energy calculations done at 16.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.67000 DelPhi exited at 13:46:15 16.668u 0.318s 0:17.27 98.2% 0+0k 0+0io 0pf+0w