Sun Oct 9 01:48:27 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 Sun Oct 9 2011 at 01:48:27 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 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: 0.5344223 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): -47.16700 7.821000 ymin,ymax (A): 177.2980 239.2080 zmin,zma (A): 77.97701 144.5910 x,y,z range (A): 54.98800 61.91000 66.61398 scale (grids/A): 0.5344223 object centre (A): -19.67300 208.2530 111.2840 number of atom coordinates read : 3398 total number of charged atoms : 3256 net assigned charge : 17.00001 assigned positive charge : 502.3725 centred at (gu) : 89.58788 89.80151 90.35144 assigned negative charge : -485.3743 centred at (gu) : 89.47607 89.83728 90.52316 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6600 nv = 96 ne = 84 npr = 65024 no. pairs analyzed = 65024 no. exposed pairs = 4644 no. arc points = 33244 no. surface atoms = 1539 nbur = 1859 mkacc time = 0.1100000 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 = 1.596000 m= 261 mr = 3222 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3408 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3344738E-09 -1.6279128E-10 midg,1,midg; midg,igrid,midg 8.8191060E-10 4.8213133E-10 1,midg,midg; igrid,midg,midg 1.5658055E-10 1.0717264E-09 gauss-seidel spectral radius is 0.9820055 estimated iterations to convergence 61 setup time was (sec) 0.4100000 now iterating at: 01:48:27 rms-change max change #iterations 6.9431886E-02 9.962755 at 10iterations 4.4638780E-03 0.8422170 at 20iterations 2.9641847E-04 4.4935226E-02 at 30iterations 2.3585631E-05 3.3149719E-03 at 40iterations 3.0791357E-06 3.0612946E-04 at 50iterations finished qdiffx linear iterations at : 01:48:30 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.0791357E-06 3.0612946E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 01:48:31 3.403u 0.185s 0:03.97 90.1% 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 Sun Oct 9 2011 at 01:48:31 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.603267 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): -47.16700 7.821000 ymin,ymax (A): 177.2980 239.2080 zmin,zma (A): 77.97701 144.5910 x,y,z range (A): 54.98800 61.91000 66.61398 scale (grids/A): 1.603267 object centre (A): -19.67300 208.2530 111.2840 number of atom coordinates read : 3398 total number of charged atoms : 3256 net assigned charge : 17.00001 assigned positive charge : 502.3725 centred at (gu) : 88.76241 89.40356 91.05322 assigned negative charge : -485.3743 centred at (gu) : 88.42786 89.51146 91.56915 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22262 mr = 47485 m= 2336 mr = 14941 m= 67 mr = 1080 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 512 time to turn everything in is 0.3600000 number of dielectric boundary points 33772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 427 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24854 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) : 0.5344223 object centre at (A) : -19.67300 208.2530 111.2840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1272682E-03 -2.1351323E-02 midg,1,midg; midg,igrid,midg 3.1856779E-02 1.9775789E-02 1,midg,midg; igrid,midg,midg 3.1232089E-03 1.7407851E-02 gauss-seidel spectral radius is 0.9981824 estimated iterations to convergence 186 setup time was (sec) 0.5800000 now iterating at: 01:48:31 rms-change max change #iterations 3.365223 163.6035 at 10iterations 1.399676 55.53156 at 20iterations 0.5813037 19.95111 at 30iterations 0.2412497 8.999432 at 40iterations 0.1004846 3.465539 at 50iterations 4.1748673E-02 1.353304 at 60iterations 1.7432367E-02 0.6714597 at 70iterations 7.2350185E-03 0.2514305 at 80iterations 3.0225879E-03 0.1062012 at 90iterations 1.2537536E-03 4.7164679E-02 at 100iterations 5.2398577E-04 1.6540527E-02 at 110iterations 2.1869500E-04 7.3080063E-03 at 120iterations finished qdiffx linear iterations at : 01:48:39 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.1869500E-04 7.3080063E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 01:48:39 7.764u 0.183s 0:08.23 96.4% 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 01:48:39 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.404901 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): -47.16700 7.821000 ymin,ymax (A): 177.2980 239.2080 zmin,zma (A): 77.97701 144.5910 x,y,z range (A): 54.98800 61.91000 66.61398 scale (grids/A): 2.404901 object centre (A): -19.67300 208.2530 111.2840 number of atom coordinates read : 3398 total number of charged atoms : 3256 net assigned charge : 17.00001 assigned positive charge : 502.3725 centred at (gu) : 88.14352 89.10513 91.57977 assigned negative charge : -485.3743 centred at (gu) : 87.64165 89.26720 92.35368 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 168709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76362 mr = 117020 m= 22114 mr = 59054 m= 3585 mr = 16347 m= 212 mr = 2242 m= 2 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1730 time to turn everything in is 0.8600000 number of dielectric boundary points 76230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 26008 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) : 1.603267 object centre at (A) : -19.67300 208.2530 111.2840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2591299 -0.3121873 midg,1,midg; midg,igrid,midg 0.4850736 0.3911668 1,midg,midg; igrid,midg,midg 5.0046798E-03 0.2412604 gauss-seidel spectral radius is 0.9991580 estimated iterations to convergence 272 setup time was (sec) 1.090000 now iterating at: 01:48:40 rms-change max change #iterations 8.915844 280.5280 at 10iterations 5.056188 136.8163 at 20iterations 2.870340 75.19585 at 30iterations 1.611838 33.54988 at 40iterations 0.9040769 21.68869 at 50iterations 0.5051602 11.39971 at 60iterations 0.2816510 5.625301 at 70iterations 0.1567603 3.189198 at 80iterations 8.7150797E-02 1.786253 at 90iterations 4.8429627E-02 1.121803 at 100iterations 2.6780197E-02 0.5720501 at 110iterations 1.4887876E-02 0.3203354 at 120iterations 8.2344580E-03 0.1797652 at 130iterations 4.5628399E-03 9.0328217E-02 at 140iterations 2.5228404E-03 4.9166679E-02 at 150iterations 1.3961507E-03 2.8319359E-02 at 160iterations 7.7319489E-04 1.5621185E-02 at 170iterations 4.2815518E-04 8.2454681E-03 at 180iterations finished qdiffx linear iterations at : 01:48:52 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 4.2815518E-04 8.2454681E-03 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 01:48:52 12.594u 0.216s 0:13.09 97.7% 0+0k 0+0io 0pf+0w