Sun Oct 9 11:36:46 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 11:36:46 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 = 2023 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: 0.6655948 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): 11.04400 52.06100 ymin,ymax (A): 52.60700 100.2550 zmin,zma (A): -30.04900 23.43700 x,y,z range (A): 41.01700 47.64801 53.48600 scale (grids/A): 0.6655948 object centre (A): 31.55250 76.43100 -3.306000 number of atom coordinates read : 2023 total number of charged atoms : 1887 net assigned charge : 4.000009 assigned positive charge : 289.5280 centred at (gu) : 90.77040 91.27933 89.45796 assigned negative charge : -285.5284 centred at (gu) : 90.78896 91.40505 89.39754 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6092 nv = 96 ne = 84 npr = 41429 no. pairs analyzed = 41429 no. exposed pairs = 2709 no. arc points = 19108 no. surface atoms = 902 nbur = 1121 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3137 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7006 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1819562E-09 1.9915408E-08 midg,1,midg; midg,igrid,midg 2.5358595E-08 -1.2215437E-08 1,midg,midg; igrid,midg,midg 1.3104272E-08 1.0567049E-08 gauss-seidel spectral radius is 0.9882542 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 11:36:47 rms-change max change #iterations 0.1463380 23.43415 at 10iterations 1.5636554E-02 2.250595 at 20iterations 1.6900320E-03 0.2529049 at 30iterations 1.8531755E-04 2.7969837E-02 at 40iterations 2.1119882E-05 2.9864311E-03 at 50iterations finished qdiffx linear iterations at : 11:36:50 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 2.1119882E-05 2.9864311E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 11:36:50 3.753u 0.267s 0:04.36 91.9% 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 11:36:50 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 = 2023 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: 1.996784 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): 11.04400 52.06100 ymin,ymax (A): 52.60700 100.2550 zmin,zma (A): -30.04900 23.43700 x,y,z range (A): 41.01700 47.64801 53.48600 scale (grids/A): 1.996784 object centre (A): 31.55250 76.43100 -3.306000 number of atom coordinates read : 2023 total number of charged atoms : 1887 net assigned charge : 4.000009 assigned positive charge : 289.5280 centred at (gu) : 92.31137 93.83804 88.37365 assigned negative charge : -285.5284 centred at (gu) : 92.36734 94.21531 88.19297 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 24541 mr = 43183 m= 5168 mr = 17824 m= 500 mr = 3464 m= 11 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14912 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) : 0.6655948 object centre at (A) : 31.55250 76.43100 -3.306000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4291279E-03 4.6468675E-03 midg,1,midg; midg,igrid,midg 2.5603186E-02 -3.4603633E-02 1,midg,midg; igrid,midg,midg 2.0722745E-02 2.2475809E-02 gauss-seidel spectral radius is 0.9987054 estimated iterations to convergence 220 setup time was (sec) 0.8800000 now iterating at: 11:36:52 rms-change max change #iterations 3.929723 212.8036 at 10iterations 1.872527 69.95267 at 20iterations 0.8899884 28.21455 at 30iterations 0.4256686 14.72080 at 40iterations 0.2035028 6.644677 at 50iterations 9.7254641E-02 3.255486 at 60iterations 4.6427555E-02 1.568352 at 70iterations 2.2220057E-02 0.7283936 at 80iterations 1.0612917E-02 0.3812828 at 90iterations 5.0698803E-03 0.1627314 at 100iterations 2.4172734E-03 8.3271027E-02 at 110iterations 1.1576987E-03 3.6948204E-02 at 120iterations finished qdiffx linear iterations at : 11:36:59 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 1.1576987E-03 3.6948204E-02 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 11:37:00 8.529u 0.274s 0:09.10 96.5% 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 11:37:00 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 = 2023 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: 2.995176 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): 11.04400 52.06100 ymin,ymax (A): 52.60700 100.2550 zmin,zma (A): -30.04900 23.43700 x,y,z range (A): 41.01700 47.64801 53.48600 scale (grids/A): 2.995176 object centre (A): 31.55250 76.43100 -3.306000 number of atom coordinates read : 2023 total number of charged atoms : 1887 net assigned charge : 4.000009 assigned positive charge : 289.5280 centred at (gu) : 93.46707 95.75707 87.56065 assigned negative charge : -285.5284 centred at (gu) : 93.55100 96.32304 87.28955 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 149243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 75383 mr = 105313 m= 31654 mr = 60387 m= 9992 mr = 25560 m= 2007 mr = 7848 m= 210 mr = 1412 m= 5 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 67860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 15096 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) : 1.996784 object centre at (A) : 31.55250 76.43100 -3.306000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2482364 9.6971229E-02 midg,1,midg; midg,igrid,midg 0.2556213 -0.4606129 1,midg,midg; igrid,midg,midg 0.2020011 0.2599286 gauss-seidel spectral radius is 0.9992730 estimated iterations to convergence 293 setup time was (sec) 1.720000 now iterating at: 11:37:02 rms-change max change #iterations 9.156619 360.8131 at 10iterations 5.362546 133.0987 at 20iterations 3.142367 72.93430 at 30iterations 1.828242 41.95892 at 40iterations 1.065194 22.50759 at 50iterations 0.6183754 12.98924 at 60iterations 0.3605907 6.415087 at 70iterations 0.2084638 3.783876 at 80iterations 0.1208296 2.200165 at 90iterations 6.9919512E-02 1.273825 at 100iterations 4.0442307E-02 0.8536854 at 110iterations 2.3363961E-02 0.4814963 at 120iterations 1.3543522E-02 0.2776017 at 130iterations 7.8188237E-03 0.1528320 at 140iterations 4.5315507E-03 8.1102371E-02 at 150iterations 2.6152702E-03 4.8807621E-02 at 160iterations 1.5107542E-03 2.9083252E-02 at 170iterations 8.7445916E-04 1.5518188E-02 at 180iterations finished qdiffx linear iterations at : 11:37:16 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 8.7445916E-04 1.5518188E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 11:37:17 16.318u 0.290s 0:16.96 97.8% 0+0k 0+0io 0pf+0w