Sat Oct 15 12:38:51 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 12:38:51 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5451 !!! WARNING: HIR 702 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5223235 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): -32.12600 27.25900 ymin,ymax (A): -13.44800 54.70900 zmin,zma (A): -30.83600 36.65700 x,y,z range (A): 59.38500 68.15700 67.49300 scale (grids/A): 0.5223235 object centre (A): -2.433499 20.63050 2.910501 number of atom coordinates read : 5451 total number of charged atoms : 5283 net assigned charge : -5.985976 assigned positive charge : 818.8653 centred at (gu) : 87.98277 89.85499 89.62975 assigned negative charge : -824.8576 centred at (gu) : 87.97396 89.76966 89.70222 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9336 nv = 96 ne = 84 npr = 111150 no. pairs analyzed = 111150 no. exposed pairs = 6877 no. arc points = 47191 no. surface atoms = 2320 nbur = 3131 mkacc time = 0.1800000 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= 331 mr = 4853 m= 0 mr = 11 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4534 ## 568 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3064875E-10 -4.5131698E-10 midg,1,midg; midg,igrid,midg -5.8197480E-10 2.5965194E-10 1,midg,midg; igrid,midg,midg -3.0774303E-10 -5.9981770E-11 gauss-seidel spectral radius is 0.9812981 estimated iterations to convergence 60 setup time was (sec) 0.5600000 now iterating at: 12:38:51 rms-change max change #iterations 8.2798697E-02 11.13984 at 10iterations 5.4583875E-03 0.8800831 at 20iterations 7.8116724E-04 0.1778297 at 30iterations 2.5531880E-04 5.8979034E-02 at 40iterations 9.1911883E-05 2.0496368E-02 at 50iterations finished qdiffx linear iterations at : 12:38:54 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 9.1911883E-05 2.0496368E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 12:38:55 3.669u 0.195s 0:04.14 92.9% 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 12:38:55 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5451 !!! WARNING: HIR 702 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.566970 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): -32.12600 27.25900 ymin,ymax (A): -13.44800 54.70900 zmin,zma (A): -30.83600 36.65700 x,y,z range (A): 59.38500 68.15700 67.49300 scale (grids/A): 1.566970 object centre (A): -2.433499 20.63050 2.910501 number of atom coordinates read : 5451 total number of charged atoms : 5283 net assigned charge : -5.985976 assigned positive charge : 818.8653 centred at (gu) : 83.94651 89.56286 88.88747 assigned negative charge : -824.8576 centred at (gu) : 83.92181 89.30852 89.10634 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 30945 mr = 72063 m= 2736 mr = 20381 m= 66 mr = 1156 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.5100000 number of dielectric boundary points 45085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 569 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 39991 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) : 0.5223235 object centre at (A) : -2.433499 20.63050 2.910501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0613343E-04 -5.6279884E-03 midg,1,midg; midg,igrid,midg -6.5313526E-03 6.3818805E-03 1,midg,midg; igrid,midg,midg -2.7250019E-03 -4.7011599E-03 gauss-seidel spectral radius is 0.9982640 estimated iterations to convergence 191 setup time was (sec) 0.7500000 now iterating at: 12:38:56 rms-change max change #iterations 4.327236 171.2134 at 10iterations 1.837296 56.86774 at 20iterations 0.7815890 24.42386 at 30iterations 0.3325644 10.30180 at 40iterations 0.1417395 4.284990 at 50iterations 6.0397461E-02 1.909092 at 60iterations 2.5754947E-02 0.7529802 at 70iterations 1.1056522E-02 0.3774400 at 80iterations 4.7942786E-03 0.1465077 at 90iterations 2.1130908E-03 7.3122025E-02 at 100iterations 9.7081013E-04 3.5007477E-02 at 110iterations 4.8749524E-04 2.0504475E-02 at 120iterations finished qdiffx linear iterations at : 12:39:03 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 4.8749524E-04 2.0504475E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 12:39:04 8.375u 0.233s 0:08.90 96.6% 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 12:39:04 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5451 !!! WARNING: HIR 702 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.350456 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): -32.12600 27.25900 ymin,ymax (A): -13.44800 54.70900 zmin,zma (A): -30.83600 36.65700 x,y,z range (A): 59.38500 68.15700 67.49300 scale (grids/A): 2.350456 object centre (A): -2.433499 20.63050 2.910501 number of atom coordinates read : 5451 total number of charged atoms : 5283 net assigned charge : -5.985976 assigned positive charge : 818.8653 centred at (gu) : 80.91933 89.34404 88.33067 assigned negative charge : -824.8576 centred at (gu) : 80.88279 88.96262 88.65930 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 244505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 110050 mr = 177123 m= 28287 mr = 85452 m= 3828 mr = 20175 m= 240 mr = 2242 m= 4 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 1.250000 number of dielectric boundary points 101833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 42166 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) : 1.566970 object centre at (A) : -2.433499 20.63050 2.910501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1902985 0.1581725 midg,1,midg; midg,igrid,midg -4.3527167E-02 7.4686967E-02 1,midg,midg; igrid,midg,midg 4.9163092E-02 -7.9849981E-02 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.520000 now iterating at: 12:39:06 rms-change max change #iterations 11.72516 293.1856 at 10iterations 6.962618 159.1064 at 20iterations 4.088685 90.71820 at 30iterations 2.388488 51.04546 at 40iterations 1.389552 28.41576 at 50iterations 0.8039180 17.28480 at 60iterations 0.4647436 7.973598 at 70iterations 0.2670779 4.709138 at 80iterations 0.1538954 2.593982 at 90iterations 8.8384882E-02 1.609674 at 100iterations 5.0682385E-02 0.9362240 at 110iterations 2.9033110E-02 0.5069923 at 120iterations 1.6636115E-02 0.2948170 at 130iterations 9.5378570E-03 0.1628647 at 140iterations 5.4678596E-03 9.9328995E-02 at 150iterations 3.1622287E-03 5.2444458E-02 at 160iterations 1.8389155E-03 3.0440331E-02 at 170iterations 1.0897469E-03 1.9292831E-02 at 180iterations finished qdiffx linear iterations at : 12:39:18 total time elapsed so far: 14.10000 # loops : 180 mean,max change (kT/e) : 1.0897469E-03 1.9292831E-02 energy calculations done at 14.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.23000 DelPhi exited at 12:39:19 14.235u 0.245s 0:14.74 98.1% 0+0k 0+0io 0pf+0w