Mon Oct 10 14:39:33 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 Mon Oct 10 2011 at 14:39:33 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 = 2845 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: 0.5659688 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 0.5659688 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 424.9790 centred at (gu) : 91.16856 87.73222 89.25763 assigned negative charge : -436.4801 centred at (gu) : 91.06625 87.75547 89.23027 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6053 nv = 96 ne = 84 npr = 56279 no. pairs analyzed = 56279 no. exposed pairs = 3847 no. arc points = 27677 no. surface atoms = 1280 nbur = 1565 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 = 1.540000 m= 243 mr = 2993 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2737 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7795 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2614295E-09 -9.8852626E-10 midg,1,midg; midg,igrid,midg -2.0738964E-09 -1.0920559E-09 1,midg,midg; igrid,midg,midg -2.2104614E-09 -2.2347599E-10 gauss-seidel spectral radius is 0.9838914 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 14:39:34 rms-change max change #iterations 8.5636273E-02 15.23060 at 10iterations 6.2989006E-03 1.097549 at 20iterations 4.9689930E-04 0.1077938 at 30iterations 5.1199557E-05 9.6340179E-03 at 40iterations 7.8022968E-06 1.8253326E-03 at 50iterations finished qdiffx linear iterations at : 14:39:37 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.8022968E-06 1.8253326E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:39:37 3.447u 0.168s 0:04.33 83.1% 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 Mon Oct 10 2011 at 14:39:38 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 = 2845 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: 1.697906 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 1.697906 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 424.9790 centred at (gu) : 93.50496 83.19557 87.77215 assigned negative charge : -436.4801 centred at (gu) : 93.19839 83.26591 87.69026 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 66955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27677 grid for indexing accessible points = 1.400000 m= 20005 mr = 44183 m= 2188 mr = 13127 m= 71 mr = 1055 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.3400000 number of dielectric boundary points 30844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20761 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) : 0.5659688 object centre at (A) : -11.48850 3.867001 18.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5201453E-02 -1.3265683E-03 midg,1,midg; midg,igrid,midg -2.1639520E-02 -1.1515648E-02 1,midg,midg; igrid,midg,midg -3.3745524E-03 -1.2849999E-02 gauss-seidel spectral radius is 0.9983188 estimated iterations to convergence 194 setup time was (sec) 0.5600000 now iterating at: 14:39:39 rms-change max change #iterations 3.558953 153.8488 at 10iterations 1.525758 60.63785 at 20iterations 0.6546745 25.82626 at 30iterations 0.2808530 10.51684 at 40iterations 0.1206445 4.551823 at 50iterations 5.1974840E-02 1.798180 at 60iterations 2.2293102E-02 0.7680969 at 70iterations 9.6034361E-03 0.3540230 at 80iterations 4.1375645E-03 0.1412964 at 90iterations 1.7928348E-03 6.1983109E-02 at 100iterations 7.7133818E-04 2.9823303E-02 at 110iterations 3.3563704E-04 1.2378693E-02 at 120iterations finished qdiffx linear iterations at : 14:39:46 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.3563704E-04 1.2378693E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:39:46 7.787u 0.210s 0:08.56 93.3% 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 Mon Oct 10 2011 at 14:39:46 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 = 2845 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: 2.546859 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 2.546859 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 424.9790 centred at (gu) : 95.25730 79.79317 86.65804 assigned negative charge : -436.4801 centred at (gu) : 94.79768 79.89870 86.53529 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27677 grid for indexing accessible points = 1.400000 m= 68845 mr = 108545 m= 19712 mr = 53376 m= 3570 mr = 14283 m= 304 mr = 2287 m= 2 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2600 time to turn everything in is 0.8200000 number of dielectric boundary points 69552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21528 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) : 1.697906 object centre at (A) : -11.48850 3.867001 18.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2128677 0.1557683 midg,1,midg; midg,igrid,midg -0.2571358 -0.1072769 1,midg,midg; igrid,midg,midg 9.6752629E-02 -0.2885485 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.060000 now iterating at: 14:39:47 rms-change max change #iterations 9.130534 308.8351 at 10iterations 5.212281 121.1781 at 20iterations 2.956604 73.28165 at 30iterations 1.666318 35.05180 at 40iterations 0.9369656 19.89366 at 50iterations 0.5254381 10.91606 at 60iterations 0.2948315 6.381149 at 70iterations 0.1650463 3.948853 at 80iterations 9.2330970E-02 1.966755 at 90iterations 5.1500596E-02 1.061099 at 100iterations 2.8768664E-02 0.5790215 at 110iterations 1.6065402E-02 0.3375554 at 120iterations 8.9655817E-03 0.1835566 at 130iterations 4.9931956E-03 9.8625183E-02 at 140iterations 2.7912455E-03 6.0258865E-02 at 150iterations 1.5597306E-03 3.1295776E-02 at 160iterations 8.7301742E-04 1.6880035E-02 at 170iterations 4.8879115E-04 9.5977783E-03 at 180iterations finished qdiffx linear iterations at : 14:39:59 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 4.8879115E-04 9.5977783E-03 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 14:39:59 12.362u 0.190s 0:12.83 97.8% 0+0k 0+0io 0pf+0w