Sat Oct 15 14:36:41 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 15 2011 at 14:36:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5791160 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 0.5791160 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4999793 assigned positive charge : 412.6473 centred at (gu) : 89.70089 89.91710 88.98516 assigned negative charge : -413.1483 centred at (gu) : 89.68376 90.10257 88.89250 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6063 nv = 96 ne = 84 npr = 55781 no. pairs analyzed = 55781 no. exposed pairs = 3504 no. arc points = 25048 no. surface atoms = 1179 nbur = 1586 mkacc time = 9.9999994E-02 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 = 1.512000 m= 280 mr = 3159 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2000000 number of dielectric boundary points 3165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2550 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4779949E-09 1.3643250E-09 midg,1,midg; midg,igrid,midg 3.5898908E-09 -3.7723158E-09 1,midg,midg; igrid,midg,midg -4.5428533E-10 2.3879290E-10 gauss-seidel spectral radius is 0.9845950 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:36:42 rms-change max change #iterations 9.4544053E-02 14.86520 at 10iterations 7.1395217E-03 1.243213 at 20iterations 5.6247669E-04 8.6358428E-02 at 30iterations 4.4024469E-05 8.1470013E-03 at 40iterations 3.4235663E-06 6.0272217E-04 at 50iterations finished qdiffx linear iterations at : 14:36:48 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 3.4235663E-06 6.0272217E-04 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 14:36:49 3.981u 0.289s 0:07.19 59.2% 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 14:36:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.737348 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 1.737348 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4999793 assigned positive charge : 412.6473 centred at (gu) : 89.10186 89.75063 86.95456 assigned negative charge : -413.1483 centred at (gu) : 89.05105 90.30718 86.67729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 66978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25048 grid for indexing accessible points = 1.400000 m= 21395 mr = 45349 m= 2643 mr = 15063 m= 108 mr = 1404 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.3600000 number of dielectric boundary points 29273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20414 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) : 0.5791160 object centre at (A) : 32.02450 35.45550 17.47150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8241434E-03 2.6157026E-03 midg,1,midg; midg,igrid,midg 1.4049462E-02 -2.2394156E-02 1,midg,midg; igrid,midg,midg 7.2920406E-03 8.8548511E-03 gauss-seidel spectral radius is 0.9983799 estimated iterations to convergence 197 setup time was (sec) 0.6300000 now iterating at: 14:36:50 rms-change max change #iterations 3.608534 147.3944 at 10iterations 1.571774 62.04149 at 20iterations 0.6850605 22.86366 at 30iterations 0.3003779 10.28134 at 40iterations 0.1308825 4.481845 at 50iterations 5.7032142E-02 2.195625 at 60iterations 2.4939727E-02 0.8317976 at 70iterations 1.0952872E-02 0.3821602 at 80iterations 4.7922558E-03 0.1766901 at 90iterations 2.0927773E-03 7.5922012E-02 at 100iterations 9.1844256E-04 3.2829285E-02 at 110iterations 4.0208394E-04 1.4793634E-02 at 120iterations finished qdiffx linear iterations at : 14:37:05 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 4.0208394E-04 1.4793634E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 14:37:06 9.329u 0.299s 0:16.88 56.9% 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 14:37:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.606022 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): 1.288000 62.76100 ymin,ymax (A): 12.06000 58.85100 zmin,zma (A): -7.319000 42.26200 x,y,z range (A): 61.47300 46.79100 49.58100 scale (grids/A): 2.606022 object centre (A): 32.02450 35.45550 17.47150 number of atom coordinates read : 2765 total number of charged atoms : 2627 net assigned charge : -0.4999793 assigned positive charge : 412.6473 centred at (gu) : 88.65255 89.62559 85.43166 assigned negative charge : -413.1483 centred at (gu) : 88.57635 90.46065 85.01586 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 155191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25048 grid for indexing accessible points = 1.400000 m= 72525 mr = 110662 m= 22560 mr = 57926 m= 4306 mr = 17274 m= 443 mr = 3007 m= 21 mr = 290 m= 0 mr = 8 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2757 time to turn everything in is 0.8800000 number of dielectric boundary points 65879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 21009 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) : 1.737348 object centre at (A) : 32.02450 35.45550 17.47150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6914594E-02 2.6024722E-02 midg,1,midg; midg,igrid,midg 0.1909673 -0.2564955 1,midg,midg; igrid,midg,midg 0.1821151 0.2875814 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 1.170000 now iterating at: 14:37:07 rms-change max change #iterations 8.974721 370.5721 at 10iterations 5.091555 125.1594 at 20iterations 2.872308 63.55304 at 30iterations 1.618009 37.54084 at 40iterations 0.9089696 18.36887 at 50iterations 0.5109300 10.03396 at 60iterations 0.2864178 5.837595 at 70iterations 0.1606970 3.048439 at 80iterations 9.0144634E-02 1.764053 at 90iterations 5.0438639E-02 1.034263 at 100iterations 2.8239025E-02 0.7155190 at 110iterations 1.5831377E-02 0.3022854 at 120iterations 8.8566123E-03 0.1767635 at 130iterations 4.9610129E-03 0.1009135 at 140iterations 2.7807911E-03 5.9307098E-02 at 150iterations 1.5571173E-03 3.1369209E-02 at 160iterations 8.6953433E-04 1.7694473E-02 at 170iterations 4.8745229E-04 9.3002319E-03 at 180iterations finished qdiffx linear iterations at : 14:37:32 total time elapsed so far: 14.16000 # loops : 180 mean,max change (kT/e) : 4.8745229E-04 9.3002319E-03 energy calculations done at 14.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.29000 DelPhi exited at 14:37:34 14.289u 0.320s 0:28.25 51.6% 0+0k 0+0io 0pf+0w