Tue Oct 11 07:54:48 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 Tue Oct 11 2011 at 07:54:48 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 = 2382 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: 0.6444722 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 0.6444722 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 89.40986 88.48288 90.59916 assigned negative charge : -352.8248 centred at (gu) : 89.32355 88.49733 90.75748 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6681 nv = 96 ne = 84 npr = 47663 no. pairs analyzed = 47663 no. exposed pairs = 2856 no. arc points = 19925 no. surface atoms = 966 nbur = 1416 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3745 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3100000 number of dielectric boundary points 3240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2023 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7916 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3042718E-08 -1.3287725E-08 midg,1,midg; midg,igrid,midg 1.2818555E-08 4.3404857E-09 1,midg,midg; igrid,midg,midg -3.2279284E-09 1.5721833E-08 gauss-seidel spectral radius is 0.9875051 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 07:54:49 rms-change max change #iterations 0.1440967 24.62058 at 10iterations 1.4944877E-02 2.246941 at 20iterations 1.5302906E-03 0.2296829 at 30iterations 1.7019598E-04 2.8276443E-02 at 40iterations 2.0985752E-05 3.5095215E-03 at 50iterations finished qdiffx linear iterations at : 07:54:53 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.0985752E-05 3.5095215E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 07:54:53 4.118u 0.272s 0:04.95 88.4% 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 Tue Oct 11 2011 at 07:54:53 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 = 2382 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: 1.933416 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 1.933416 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 88.22905 85.44823 91.79716 assigned negative charge : -352.8248 centred at (gu) : 87.97054 85.49177 92.27248 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19925 grid for indexing accessible points = 1.400000 m= 27285 mr = 50418 m= 4628 mr = 20691 m= 333 mr = 3072 m= 3 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1370 time to turn everything in is 0.6400000 number of dielectric boundary points 29751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17669 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) : 0.6444722 object centre at (A) : 15.51150 13.29150 29.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2609002E-02 -2.1642042E-02 midg,1,midg; midg,igrid,midg 2.6782930E-02 1.9720353E-02 1,midg,midg; igrid,midg,midg -4.3501160E-03 6.2958780E-03 gauss-seidel spectral radius is 0.9986508 estimated iterations to convergence 216 setup time was (sec) 0.9500000 now iterating at: 07:54:55 rms-change max change #iterations 4.100901 182.9139 at 10iterations 1.929461 71.29196 at 20iterations 0.9119812 33.02191 at 30iterations 0.4301985 16.10061 at 40iterations 0.2031062 6.529423 at 50iterations 9.5332690E-02 3.417908 at 60iterations 4.5054492E-02 1.338959 at 70iterations 2.1287119E-02 0.7435350 at 80iterations 1.0039413E-02 0.2990265 at 90iterations 4.7486592E-03 0.1529245 at 100iterations 2.2429707E-03 7.5273514E-02 at 110iterations 1.0642416E-03 3.3734322E-02 at 120iterations finished qdiffx linear iterations at : 07:55:03 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.0642416E-03 3.3734322E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 07:55:04 9.566u 0.311s 0:10.26 96.1% 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 Tue Oct 11 2011 at 07:55:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 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: 2.900125 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 2.900125 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 87.34354 83.17216 92.69585 assigned negative charge : -352.8248 centred at (gu) : 86.95582 83.23756 93.40861 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 165981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19925 grid for indexing accessible points = 1.400000 m= 87143 mr = 121911 m= 32965 mr = 72397 m= 8505 mr = 26967 m= 1410 mr = 6715 m= 132 mr = 1038 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 4962 time to turn everything in is 1.680000 number of dielectric boundary points 67028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 17956 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) : 1.933416 object centre at (A) : 15.51150 13.29150 29.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4799499 -0.3401711 midg,1,midg; midg,igrid,midg 0.1933892 0.2278549 1,midg,midg; igrid,midg,midg -3.4682442E-02 -1.4964278E-03 gauss-seidel spectral radius is 0.9992556 estimated iterations to convergence 289 setup time was (sec) 2.020000 now iterating at: 07:55:06 rms-change max change #iterations 9.642880 470.8536 at 10iterations 5.641287 164.0233 at 20iterations 3.274687 69.31923 at 30iterations 1.898092 41.81439 at 40iterations 1.097348 22.82645 at 50iterations 0.6325148 13.90388 at 60iterations 0.3642227 7.101829 at 70iterations 0.2099748 4.321348 at 80iterations 0.1206296 2.245510 at 90iterations 6.9378465E-02 1.308228 at 100iterations 3.9898530E-02 0.8023648 at 110iterations 2.2864128E-02 0.4106750 at 120iterations 1.3157258E-02 0.2375774 at 130iterations 7.5528333E-03 0.1416159 at 140iterations 4.3378780E-03 7.4457169E-02 at 150iterations 2.4994758E-03 4.7647238E-02 at 160iterations 1.4414046E-03 2.6985168E-02 at 170iterations 8.3758333E-04 1.4678955E-02 at 180iterations finished qdiffx linear iterations at : 07:55:20 total time elapsed so far: 15.87000 # loops : 180 mean,max change (kT/e) : 8.3758333E-04 1.4678955E-02 energy calculations done at 15.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.05000 DelPhi exited at 07:55:20 16.055u 0.309s 0:16.69 97.9% 0+0k 0+0io 0pf+0w