Sat Oct 8 19:45:20 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 19:45:20 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6170592 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 0.6170592 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 88.47600 88.60573 89.60883 assigned negative charge : -390.1886 centred at (gu) : 88.37418 88.68195 89.49942 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6397 nv = 96 ne = 84 npr = 54210 no. pairs analyzed = 54210 no. exposed pairs = 3004 no. arc points = 21604 no. surface atoms = 1008 nbur = 1580 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3566 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3300000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2165 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4869877E-09 8.4917495E-09 midg,1,midg; midg,igrid,midg 9.9332187E-09 -1.4522109E-09 1,midg,midg; igrid,midg,midg -5.1908211E-09 6.3001280E-09 gauss-seidel spectral radius is 0.9863952 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 19:45:21 rms-change max change #iterations 0.1243133 19.96149 at 10iterations 1.1554232E-02 1.773432 at 20iterations 1.0490170E-03 0.1504269 at 30iterations 9.4346113E-05 1.4217377E-02 at 40iterations 8.6207401E-06 1.2321472E-03 at 50iterations finished qdiffx linear iterations at : 19:45:25 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 8.6207401E-06 1.2321472E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 19:45:25 4.775u 0.371s 0:05.42 94.8% 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 19:45:25 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.851178 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 1.851178 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 85.42755 85.81673 88.82590 assigned negative charge : -390.1886 centred at (gu) : 85.12244 86.04567 88.49805 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 23689 mr = 48387 m= 3214 mr = 17390 m= 147 mr = 1895 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4589 time to turn everything in is 0.5600000 number of dielectric boundary points 28884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19224 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) : 0.6170592 object centre at (A) : 14.16200 2.401000 16.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9725388E-02 2.3160648E-02 midg,1,midg; midg,igrid,midg 1.9532239E-02 5.8491901E-03 1,midg,midg; igrid,midg,midg -4.5352960E-03 3.0924486E-02 gauss-seidel spectral radius is 0.9985511 estimated iterations to convergence 208 setup time was (sec) 0.8600000 now iterating at: 19:45:26 rms-change max change #iterations 4.013389 159.6960 at 10iterations 1.835104 67.19784 at 20iterations 0.8387422 29.36427 at 30iterations 0.3832510 12.30053 at 40iterations 0.1764658 5.794804 at 50iterations 8.0662951E-02 2.875242 at 60iterations 3.6921147E-02 1.301003 at 70iterations 1.6811199E-02 0.5705013 at 80iterations 7.7202544E-03 0.2674255 at 90iterations 3.5450940E-03 0.1300888 at 100iterations 1.6189517E-03 5.1343918E-02 at 110iterations 7.4191805E-04 2.4213791E-02 at 120iterations finished qdiffx linear iterations at : 19:45:36 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 7.4191805E-04 2.4213791E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.53000 DelPhi exited at 19:45:36 10.533u 0.465s 0:11.25 97.6% 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 8 2011 at 19:45:36 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIR 91 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: HIR 116 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.776767 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): -10.49500 38.81900 ymin,ymax (A): -22.05900 26.86100 zmin,zma (A): -12.53200 45.16100 x,y,z range (A): 49.31400 48.92000 57.69300 scale (grids/A): 2.776767 object centre (A): 14.16200 2.401000 16.31450 number of atom coordinates read : 2588 total number of charged atoms : 2453 net assigned charge : 3.542005 assigned positive charge : 393.7300 centred at (gu) : 83.14120 83.72482 88.23887 assigned negative charge : -390.1886 centred at (gu) : 82.68362 84.06853 87.74709 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21604 grid for indexing accessible points = 1.400000 m= 78537 mr = 117179 m= 25825 mr = 64397 m= 5498 mr = 20581 m= 653 mr = 4049 m= 29 mr = 424 m= 0 mr = 8 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 15942 time to turn everything in is 1.430000 number of dielectric boundary points 65017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19621 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) : 1.851178 object centre at (A) : 14.16200 2.401000 16.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1459907 0.2708818 midg,1,midg; midg,igrid,midg 0.2309738 0.1406855 1,midg,midg; igrid,midg,midg -1.8225122E-02 0.3890462 gauss-seidel spectral radius is 0.9992289 estimated iterations to convergence 284 setup time was (sec) 1.750000 now iterating at: 19:45:39 rms-change max change #iterations 9.459414 345.5942 at 10iterations 5.423728 190.0024 at 20iterations 3.093228 82.31419 at 30iterations 1.761928 45.77500 at 40iterations 1.002159 20.72100 at 50iterations 0.5704398 12.15520 at 60iterations 0.3245715 6.317277 at 70iterations 0.1842119 4.216906 at 80iterations 0.1043611 1.930391 at 90iterations 5.9309941E-02 1.169670 at 100iterations 3.3719588E-02 0.6373739 at 110iterations 1.9109566E-02 0.3858337 at 120iterations 1.0830179E-02 0.2314014 at 130iterations 6.1407890E-03 0.1072617 at 140iterations 3.4894929E-03 6.8561554E-02 at 150iterations 1.9824882E-03 3.9237976E-02 at 160iterations 1.1236310E-03 2.0490646E-02 at 170iterations 6.3709659E-04 1.3336182E-02 at 180iterations finished qdiffx linear iterations at : 19:45:55 total time elapsed so far: 18.08000 # loops : 180 mean,max change (kT/e) : 6.3709659E-04 1.3336182E-02 energy calculations done at 18.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 19:45:55 18.249u 0.480s 0:19.03 98.3% 0+0k 0+0io 0pf+0w