Sat Oct 8 15:47:54 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 Sat Oct 8 2011 at 15:47:54 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 = 2436 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: 0.6555445 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 0.6555445 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.500000 assigned positive charge : 358.7549 centred at (gu) : 90.21911 88.82201 90.50689 assigned negative charge : -354.2557 centred at (gu) : 90.17240 88.99004 90.55893 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6960 nv = 96 ne = 84 npr = 49908 no. pairs analyzed = 49908 no. exposed pairs = 3011 no. arc points = 21039 no. surface atoms = 1040 nbur = 1396 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3837 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2900000 number of dielectric boundary points 3508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6339587E-08 1.4928672E-09 midg,1,midg; midg,igrid,midg 4.6671911E-08 -1.3671221E-08 1,midg,midg; igrid,midg,midg 2.1893185E-09 1.8095875E-08 gauss-seidel spectral radius is 0.9879261 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 15:47:55 rms-change max change #iterations 0.1517898 21.11530 at 10iterations 1.6328651E-02 2.302864 at 20iterations 1.7480616E-03 0.2487717 at 30iterations 2.2713737E-04 3.2719612E-02 at 40iterations 4.5640154E-05 6.1213970E-03 at 50iterations finished qdiffx linear iterations at : 15:47:59 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 4.5640154E-05 6.1213970E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 15:47:59 4.452u 0.405s 0:05.14 94.3% 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 Sat Oct 8 2011 at 15:47:59 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 = 2436 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: 1.966634 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 1.966634 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.500000 assigned positive charge : 358.7549 centred at (gu) : 90.65683 86.46549 91.52015 assigned negative charge : -354.2557 centred at (gu) : 90.51705 86.97005 91.67648 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21039 grid for indexing accessible points = 1.400000 m= 29029 mr = 51468 m= 5891 mr = 21702 m= 448 mr = 4037 m= 11 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1067 time to turn everything in is 0.6100000 number of dielectric boundary points 32100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18436 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) : 0.6555445 object centre at (A) : 48.59400 39.87550 9.063000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9277079E-02 -1.9916052E-02 midg,1,midg; midg,igrid,midg 3.6473647E-02 -5.8590649E-03 1,midg,midg; igrid,midg,midg 7.8364564E-03 -3.0208987E-04 gauss-seidel spectral radius is 0.9986992 estimated iterations to convergence 220 setup time was (sec) 0.9200000 now iterating at: 15:48:01 rms-change max change #iterations 4.293884 182.8712 at 10iterations 2.040465 77.95485 at 20iterations 0.9728234 30.21841 at 30iterations 0.4627891 14.03113 at 40iterations 0.2205761 7.203894 at 50iterations 0.1051650 3.473099 at 60iterations 5.0332159E-02 1.461845 at 70iterations 2.4022050E-02 0.7755165 at 80iterations 1.1467381E-02 0.3714180 at 90iterations 5.4948973E-03 0.1692381 at 100iterations 2.6393097E-03 8.4047318E-02 at 110iterations 1.2705663E-03 4.1526794E-02 at 120iterations finished qdiffx linear iterations at : 15:48:10 total time elapsed so far: 10.35000 # loops : 120 mean,max change (kT/e) : 1.2705663E-03 4.1526794E-02 energy calculations done at 10.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.52000 DelPhi exited at 15:48:10 10.521u 0.463s 0:11.23 97.7% 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 Sat Oct 8 2011 at 15:48:11 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 = 2436 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: 2.949950 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): 23.34800 73.84000 ymin,ymax (A): 17.48300 62.26800 zmin,zma (A): -18.09000 36.21600 x,y,z range (A): 50.49200 44.78500 54.30600 scale (grids/A): 2.949950 object centre (A): 48.59400 39.87550 9.063000 number of atom coordinates read : 2436 total number of charged atoms : 2335 net assigned charge : 4.500000 assigned positive charge : 358.7549 centred at (gu) : 90.98512 84.69801 92.27988 assigned negative charge : -354.2557 centred at (gu) : 90.77549 85.45495 92.51464 start vw surface at 0.1100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 171130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21039 grid for indexing accessible points = 1.400000 m= 89829 mr = 124611 m= 37605 mr = 73787 m= 11207 mr = 30906 m= 2001 mr = 8822 m= 190 mr = 1377 m= 4 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 3623 time to turn everything in is 1.660000 number of dielectric boundary points 72378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 18676 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) : 1.966634 object centre at (A) : 48.59400 39.87550 9.063000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2045829 -0.2470687 midg,1,midg; midg,igrid,midg 0.2530442 -8.2765542E-02 1,midg,midg; igrid,midg,midg 9.6693829E-02 -0.1106786 gauss-seidel spectral radius is 0.9992732 estimated iterations to convergence 293 setup time was (sec) 2.010000 now iterating at: 15:48:13 rms-change max change #iterations 10.04731 369.4136 at 10iterations 5.907512 177.2585 at 20iterations 3.463338 79.34389 at 30iterations 2.028159 42.51381 at 40iterations 1.182878 24.69462 at 50iterations 0.6881854 12.46173 at 60iterations 0.3997885 7.775391 at 70iterations 0.2322370 4.297901 at 80iterations 0.1346760 2.279596 at 90iterations 7.8015260E-02 1.354298 at 100iterations 4.5228411E-02 0.8435059 at 110iterations 2.6130363E-02 0.4796948 at 120iterations 1.5133142E-02 0.2653050 at 130iterations 8.7775709E-03 0.1559525 at 140iterations 5.1066675E-03 8.4016800E-02 at 150iterations 2.9655944E-03 5.4183960E-02 at 160iterations 1.7419198E-03 3.2617569E-02 at 170iterations 1.0331726E-03 1.8270493E-02 at 180iterations finished qdiffx linear iterations at : 15:48:29 total time elapsed so far: 17.79000 # loops : 180 mean,max change (kT/e) : 1.0331726E-03 1.8270493E-02 energy calculations done at 17.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.96000 DelPhi exited at 15:48:29 17.966u 0.480s 0:18.75 98.3% 0+0k 0+0io 0pf+0w