Mon Oct 10 14:12:46 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 Mon Oct 10 2011 at 14:12:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5616736 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 0.5616736 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.1116266E-05 assigned positive charge : 394.5128 centred at (gu) : 90.05727 90.09278 91.20894 assigned negative charge : -394.5132 centred at (gu) : 90.12386 90.15807 91.38583 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5569 nv = 96 ne = 84 npr = 54940 no. pairs analyzed = 54940 no. exposed pairs = 3544 no. arc points = 25829 no. surface atoms = 1182 nbur = 1529 mkacc time = 0.1600000 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= 223 mr = 2734 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.4000000 number of dielectric boundary points 3055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2687 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3647665E-09 -2.5020861E-09 midg,1,midg; midg,igrid,midg 6.8738948E-10 -6.7230072E-10 1,midg,midg; igrid,midg,midg 7.0648015E-10 -6.8036632E-10 gauss-seidel spectral radius is 0.9836317 estimated iterations to convergence 64 setup time was (sec) 0.7000000 now iterating at: 14:12:47 rms-change max change #iterations 7.9983957E-02 14.29385 at 10iterations 5.7028751E-03 0.9291220 at 20iterations 4.0484156E-04 7.7642441E-02 at 30iterations 2.8691587E-05 5.1136017E-03 at 40iterations 2.0840341E-06 3.1566620E-04 at 50iterations finished qdiffx linear iterations at : 14:12:50 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 2.0840341E-06 3.1566620E-04 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 14:12:51 4.308u 0.202s 0:05.05 89.1% 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 14:12:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.685021 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 1.685021 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.1116266E-05 assigned positive charge : 394.5128 centred at (gu) : 90.17101 90.27798 93.62614 assigned negative charge : -394.5132 centred at (gu) : 90.37122 90.47380 94.15702 start vw surface at 0.2400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 61827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25829 grid for indexing accessible points = 1.400000 m= 17895 mr = 40510 m= 1792 mr = 11699 m= 58 mr = 787 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2030 time to turn everything in is 0.6300000 number of dielectric boundary points 28576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19906 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) : 0.5616736 object centre at (A) : -15.93000 13.92450 -10.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5629656E-02 -3.2972798E-02 midg,1,midg; midg,igrid,midg 3.5018395E-03 -1.4061170E-03 1,midg,midg; igrid,midg,midg 5.5093118E-03 -1.7727362E-02 gauss-seidel spectral radius is 0.9982654 estimated iterations to convergence 191 setup time was (sec) 0.9800000 now iterating at: 14:12:52 rms-change max change #iterations 3.314732 151.0535 at 10iterations 1.406873 54.59257 at 20iterations 0.5969958 22.69361 at 30iterations 0.2531275 9.435471 at 40iterations 0.1074467 3.894773 at 50iterations 4.5659099E-02 1.619610 at 60iterations 1.9336928E-02 0.6713715 at 70iterations 8.2126530E-03 0.3099518 at 80iterations 3.4865504E-03 0.1270436 at 90iterations 1.4822774E-03 5.6447983E-02 at 100iterations 6.3088851E-04 2.4636313E-02 at 110iterations 2.6805003E-04 1.0163784E-02 at 120iterations finished qdiffx linear iterations at : 14:13:00 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 2.6805003E-04 1.0163784E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 14:13:01 9.419u 0.245s 0:10.18 94.7% 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 Mon Oct 10 2011 at 14:13:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.527531 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): -42.64800 10.78800 ymin,ymax (A): -7.097000 34.94600 zmin,zma (A): -42.24900 21.13300 x,y,z range (A): 53.43600 42.04300 63.38200 scale (grids/A): 2.527531 object centre (A): -15.93000 13.92450 -10.55800 number of atom coordinates read : 2711 total number of charged atoms : 2576 net assigned charge : 1.1116266E-05 assigned positive charge : 394.5128 centred at (gu) : 90.25660 90.41689 95.43908 assigned negative charge : -394.5132 centred at (gu) : 90.55673 90.71066 96.23541 start vw surface at 0.2000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 143792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25829 grid for indexing accessible points = 1.400000 m= 62546 mr = 99833 m= 16585 mr = 48137 m= 2767 mr = 11760 m= 207 mr = 1679 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 6616 time to turn everything in is 1.350000 number of dielectric boundary points 64428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 20593 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) : 1.685021 object centre at (A) : -15.93000 13.92450 -10.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4051116 -0.5762944 midg,1,midg; midg,igrid,midg 3.7138052E-02 -3.5429064E-02 1,midg,midg; igrid,midg,midg 8.0114529E-02 -0.2827843 gauss-seidel spectral radius is 0.9991552 estimated iterations to convergence 272 setup time was (sec) 1.740000 now iterating at: 14:13:03 rms-change max change #iterations 8.379472 348.9183 at 10iterations 4.718619 114.1923 at 20iterations 2.631432 62.55214 at 30iterations 1.463558 35.82555 at 40iterations 0.8130532 17.57909 at 50iterations 0.4497120 11.44002 at 60iterations 0.2496538 5.319915 at 70iterations 0.1377422 3.026122 at 80iterations 7.6097943E-02 1.743343 at 90iterations 4.2148639E-02 1.018209 at 100iterations 2.3250367E-02 0.4648876 at 110iterations 1.2817693E-02 0.2750473 at 120iterations 7.0672813E-03 0.1575584 at 130iterations 3.9086593E-03 7.8888059E-02 at 140iterations 2.1563242E-03 4.4860840E-02 at 150iterations 1.1900165E-03 2.7423859E-02 at 160iterations 6.5540086E-04 1.3235092E-02 at 170iterations 3.6254578E-04 7.6150894E-03 at 180iterations finished qdiffx linear iterations at : 14:13:16 total time elapsed so far: 14.32000 # loops : 180 mean,max change (kT/e) : 3.6254578E-04 7.6150894E-03 energy calculations done at 14.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 14:13:16 14.564u 0.247s 0:15.29 96.7% 0+0k 0+0io 0pf+0w