Sun Oct 9 15:26:43 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 Sun Oct 9 2011 at 15:26:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4587275 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): 8.917999 62.43400 ymin,ymax (A): 53.96600 131.5720 zmin,zma (A): 29.55600 96.67200 x,y,z range (A): 53.51600 77.60599 67.11600 scale (grids/A): 0.4587275 object centre (A): 35.67600 92.76900 63.11400 number of atom coordinates read : 5439 total number of charged atoms : 5274 net assigned charge : 5.000036 assigned positive charge : 846.0903 centred at (gu) : 89.57447 89.43049 90.67879 assigned negative charge : -841.0978 centred at (gu) : 89.57624 89.37386 90.58415 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6749 nv = 96 ne = 84 npr = 109333 no. pairs analyzed = 109333 no. exposed pairs = 6604 no. arc points = 45760 no. surface atoms = 2220 nbur = 3219 mkacc time = 0.2900000 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 = 1.876000 m= 204 mr = 3405 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 3548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4096 ## 797 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 9354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5941136E-11 3.6028833E-11 midg,1,midg; midg,igrid,midg -1.1224886E-11 1.6843724E-11 1,midg,midg; igrid,midg,midg 6.5464604E-12 4.3305069E-12 gauss-seidel spectral radius is 0.9757708 estimated iterations to convergence 53 setup time was (sec) 0.8900000 now iterating at: 15:26:44 rms-change max change #iterations 4.0619906E-02 6.750628 at 10iterations 2.6760271E-03 0.4024582 at 20iterations 6.4510544E-04 9.9632263E-02 at 30iterations 1.9876314E-04 3.4487724E-02 at 40iterations 6.2246290E-05 1.1506081E-02 at 50iterations finished qdiffx linear iterations at : 15:26:49 total time elapsed so far: 5.560000 # loops : 50 mean,max change (kT/e) : 6.2246290E-05 1.1506081E-02 energy calculations done at 5.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.750000 DelPhi exited at 15:26:50 5.755u 0.451s 0:06.47 95.8% 0+0k 0+0io 6pf+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 15:26:50 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 = 5439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.376182 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): 8.917999 62.43400 ymin,ymax (A): 53.96600 131.5720 zmin,zma (A): 29.55600 96.67200 x,y,z range (A): 53.51600 77.60599 67.11600 scale (grids/A): 1.376182 object centre (A): 35.67600 92.76900 63.11400 number of atom coordinates read : 5439 total number of charged atoms : 5274 net assigned charge : 5.000036 assigned positive charge : 846.0903 centred at (gu) : 88.72147 88.28981 92.03416 assigned negative charge : -841.0978 centred at (gu) : 88.72839 88.12143 91.75222 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45760 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 19679 mr = 53648 m= 1158 mr = 12389 m= 12 mr = 327 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1330 time to turn everything in is 0.7100000 number of dielectric boundary points 33288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 798 ## 24 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 37811 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) : 0.4587275 object centre at (A) : 35.67600 92.76900 63.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5836506E-03 5.0844373E-03 midg,1,midg; midg,igrid,midg -3.3251462E-03 8.5501289E-03 1,midg,midg; igrid,midg,midg 7.1418472E-04 1.4732890E-03 gauss-seidel spectral radius is 0.9976430 estimated iterations to convergence 164 setup time was (sec) 1.110000 now iterating at: 15:26:51 rms-change max change #iterations 3.178903 123.6656 at 10iterations 1.174193 42.14606 at 20iterations 0.4327493 15.60187 at 30iterations 0.1607047 5.980728 at 40iterations 5.9537914E-02 1.954592 at 50iterations 2.2193171E-02 0.7703154 at 60iterations 8.2723759E-03 0.2811432 at 70iterations 3.1790596E-03 0.1100178 at 80iterations 1.2890631E-03 4.7767639E-02 at 90iterations 5.8360316E-04 2.1858692E-02 at 100iterations 3.0570145E-04 1.1442184E-02 at 110iterations 1.8033646E-04 7.1334839E-03 at 120iterations finished qdiffx linear iterations at : 15:27:03 total time elapsed so far: 12.54000 # loops : 120 mean,max change (kT/e) : 1.8033646E-04 7.1334839E-03 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 15:27:03 12.718u 0.520s 0:13.51 97.9% 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 15:27:03 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 = 5439 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.064274 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): 8.917999 62.43400 ymin,ymax (A): 53.96600 131.5720 zmin,zma (A): 29.55600 96.67200 x,y,z range (A): 53.51600 77.60599 67.11600 scale (grids/A): 2.064274 object centre (A): 35.67600 92.76900 63.11400 number of atom coordinates read : 5439 total number of charged atoms : 5274 net assigned charge : 5.000036 assigned positive charge : 846.0903 centred at (gu) : 88.08176 87.43431 93.05087 assigned negative charge : -841.0978 centred at (gu) : 88.09252 87.18189 92.62849 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 184610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45760 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 74462 mr = 132802 m= 14916 mr = 56809 m= 1352 mr = 10065 m= 35 mr = 645 m= 0 mr = 7 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 4407 time to turn everything in is 1.660000 number of dielectric boundary points 75047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 41834 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) : 1.376182 object centre at (A) : 35.67600 92.76900 63.11400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0754071E-02 4.1666254E-02 midg,1,midg; midg,igrid,midg -0.1186704 0.1730081 1,midg,midg; igrid,midg,midg 1.8123562E-02 3.8014673E-02 gauss-seidel spectral radius is 0.9990222 estimated iterations to convergence 253 setup time was (sec) 2.060000 now iterating at: 15:27:06 rms-change max change #iterations 9.275305 246.8258 at 10iterations 5.038298 122.9532 at 20iterations 2.725909 70.98695 at 30iterations 1.470736 36.18128 at 40iterations 0.7874949 19.06532 at 50iterations 0.4217723 9.807014 at 60iterations 0.2252620 5.174355 at 70iterations 0.1197150 2.558732 at 80iterations 6.3702628E-02 1.290556 at 90iterations 3.3846214E-02 0.7517014 at 100iterations 1.8015999E-02 0.3982239 at 110iterations 9.5531158E-03 0.1849556 at 120iterations 5.0685685E-03 0.1003857 at 130iterations 2.6951167E-03 5.5068970E-02 at 140iterations 1.4341528E-03 2.8404236E-02 at 150iterations 7.6928118E-04 1.6021729E-02 at 160iterations 4.1622546E-04 8.5034370E-03 at 170iterations 2.2881375E-04 4.7307014E-03 at 180iterations finished qdiffx linear iterations at : 15:27:25 total time elapsed so far: 21.40000 # loops : 180 mean,max change (kT/e) : 2.2881375E-04 4.7307014E-03 energy calculations done at 21.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.57000 DelPhi exited at 15:27:26 21.579u 0.565s 0:22.43 98.6% 0+0k 0+0io 0pf+0w