Sun Oct 9 08:19:06 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 Sun Oct 9 2011 at 08:19:06 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 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: 0.4805162 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 0.4805162 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 895.5120 centred at (gu) : 88.41160 89.60047 89.59229 assigned negative charge : -896.0197 centred at (gu) : 88.40381 89.43102 89.59850 start vw surface at 0.2900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 8463 nv = 96 ne = 84 npr = 120920 no. pairs analyzed = 120920 no. exposed pairs = 7300 no. arc points = 50561 no. surface atoms = 2462 nbur = 3489 mkacc time = 0.3500000 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 = 1.764000 m= 239 mr = 4320 m= 0 mr = 2 time to grow re-entrant surface = 0.3799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 4380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4810 ## 838 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 11595 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7904224E-12 -5.3671000E-12 midg,1,midg; midg,igrid,midg -1.6177600E-10 1.2147203E-10 1,midg,midg; igrid,midg,midg -1.1478622E-11 3.5431144E-12 gauss-seidel spectral radius is 0.9779432 estimated iterations to convergence 56 setup time was (sec) 1.010000 now iterating at: 08:19:08 rms-change max change #iterations 5.6241214E-02 10.36029 at 10iterations 2.7131692E-03 0.4603078 at 20iterations 1.4460523E-04 2.3300171E-02 at 30iterations 1.7607084E-05 3.0879974E-03 at 40iterations 4.8229876E-06 7.6866150E-04 at 50iterations finished qdiffx linear iterations at : 08:19:11 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 4.8229876E-06 7.6866150E-04 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.730000 DelPhi exited at 08:19:12 4.730u 0.263s 0:05.46 91.3% 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 Sun Oct 9 2011 at 08:19:12 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 1.441548 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 1.441548 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 895.5120 centred at (gu) : 85.23272 88.79971 88.77470 assigned negative charge : -896.0197 centred at (gu) : 85.21088 88.29276 88.79509 start vw surface at 0.2900000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 98079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50561 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 25441 mr = 67574 m= 1604 mr = 16141 m= 25 mr = 508 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 319 time to turn everything in is 0.9000000 number of dielectric boundary points 40926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 850 ## 16 charges are in solution ## iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 42468 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) : 0.4805162 object centre at (A) : -2.839001 23.59250 6.571000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8034303E-03 1.6466187E-03 midg,1,midg; midg,igrid,midg -2.4011468E-03 2.1627543E-02 1,midg,midg; igrid,midg,midg -7.8306900E-04 -2.8774486E-04 gauss-seidel spectral radius is 0.9979399 estimated iterations to convergence 175 setup time was (sec) 1.290000 now iterating at: 08:19:13 rms-change max change #iterations 3.730874 131.5332 at 10iterations 1.471340 54.47396 at 20iterations 0.5798957 19.21104 at 30iterations 0.2292036 7.432022 at 40iterations 9.0355091E-02 2.728883 at 50iterations 3.5706293E-02 1.213118 at 60iterations 1.4076936E-02 0.4513702 at 70iterations 5.6040697E-03 0.1911430 at 80iterations 2.2290600E-03 7.2860718E-02 at 90iterations 8.9041010E-04 2.7986526E-02 at 100iterations 3.6292127E-04 1.1711121E-02 at 110iterations 1.5451142E-04 5.5875778E-03 at 120iterations finished qdiffx linear iterations at : 08:19:22 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 1.5451142E-04 5.5875778E-03 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.30000 DelPhi exited at 08:19:23 10.300u 0.275s 0:11.02 95.9% 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 Sun Oct 9 2011 at 08:19:23 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 2.162323 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 2.162323 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 895.5120 centred at (gu) : 82.84868 88.19941 88.16161 assigned negative charge : -896.0197 centred at (gu) : 82.81624 87.43909 88.19249 start vw surface at 0.2900000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 229754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50561 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96100 mr = 167391 m= 20144 mr = 73674 m= 1959 mr = 13614 m= 58 mr = 976 m= 0 mr = 9 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 1148 time to turn everything in is 2.120000 number of dielectric boundary points 92351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 45978 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) : 1.441548 object centre at (A) : -2.839001 23.59250 6.571000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1683304 8.1116511E-03 midg,1,midg; midg,igrid,midg 0.1245546 0.6292784 1,midg,midg; igrid,midg,midg 3.3176318E-02 7.0974920E-03 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 2.550000 now iterating at: 08:19:26 rms-change max change #iterations 10.66641 288.0744 at 10iterations 6.094142 146.2539 at 20iterations 3.471211 80.65833 at 30iterations 1.962918 41.41275 at 40iterations 1.103565 22.74686 at 50iterations 0.6202658 14.12797 at 60iterations 0.3483404 6.689980 at 70iterations 0.1942594 3.680106 at 80iterations 0.1080168 2.243987 at 90iterations 6.0151819E-02 0.9996872 at 100iterations 3.3452146E-02 0.6683826 at 110iterations 1.8588021E-02 0.3287544 at 120iterations 1.0306182E-02 0.1998610 at 130iterations 5.7163518E-03 0.1045694 at 140iterations 3.1722875E-03 5.9298158E-02 at 150iterations 1.7565918E-03 3.3111572E-02 at 160iterations 9.7311486E-04 1.8885612E-02 at 170iterations 5.4047047E-04 1.0036469E-02 at 180iterations finished qdiffx linear iterations at : 08:19:40 total time elapsed so far: 16.85000 # loops : 180 mean,max change (kT/e) : 5.4047047E-04 1.0036469E-02 energy calculations done at 16.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.08000 DelPhi exited at 08:19:41 17.085u 0.286s 0:17.67 98.2% 0+0k 0+0io 0pf+0w