Sat Oct 15 14:14:33 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 Sat Oct 15 2011 at 14:14:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4638 !!! WARNING: HEM 807 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5204526 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): -24.71500 38.94200 ymin,ymax (A): -17.63100 45.00900 zmin,zma (A): 6.715000 75.11700 x,y,z range (A): 63.65700 62.64000 68.40201 scale (grids/A): 0.5204526 object centre (A): 7.113501 13.68900 40.91600 number of atom coordinates read : 4638 total number of charged atoms : 4398 net assigned charge : 7.300036 assigned positive charge : 700.9634 centred at (gu) : 91.47505 89.06779 87.81727 assigned negative charge : -693.6675 centred at (gu) : 91.58740 89.17882 87.69028 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7969 nv = 96 ne = 84 npr = 92398 no. pairs analyzed = 92398 no. exposed pairs = 6206 no. arc points = 42782 no. surface atoms = 2065 nbur = 2573 mkacc time = 0.1500000 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 = 1.624000 m= 323 mr = 3962 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4112 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10567 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6816335E-10 3.6750511E-10 midg,1,midg; midg,igrid,midg 7.4640083E-10 -1.9547378E-10 1,midg,midg; igrid,midg,midg 4.0357553E-10 -3.8337206E-10 gauss-seidel spectral radius is 0.9811121 estimated iterations to convergence 60 setup time was (sec) 0.5100000 now iterating at: 14:14:34 rms-change max change #iterations 7.2334729E-02 12.40054 at 10iterations 5.0889966E-03 1.000458 at 20iterations 1.0657544E-03 0.1490555 at 30iterations 4.0994864E-04 6.0952663E-02 at 40iterations 1.6741735E-04 2.5893211E-02 at 50iterations finished qdiffx linear iterations at : 14:14:43 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.6741735E-04 2.5893211E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:14:44 3.744u 0.198s 0:11.09 35.4% 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 Sat Oct 15 2011 at 14:14:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4638 !!! WARNING: HEM 807 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.561358 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): -24.71500 38.94200 ymin,ymax (A): -17.63100 45.00900 zmin,zma (A): 6.715000 75.11700 x,y,z range (A): 63.65700 62.64000 68.40201 scale (grids/A): 1.561358 object centre (A): 7.113501 13.68900 40.91600 number of atom coordinates read : 4638 total number of charged atoms : 4398 net assigned charge : 7.300036 assigned positive charge : 700.9634 centred at (gu) : 94.42333 87.20218 83.45036 assigned negative charge : -693.6675 centred at (gu) : 94.76189 87.53605 83.07063 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42782 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27571 mr = 59529 m= 2584 mr = 18490 m= 47 mr = 1104 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.4500000 number of dielectric boundary points 40288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 479 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33217 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) : 0.5204526 object centre at (A) : 7.113501 13.68900 40.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9190984E-03 2.1238193E-02 midg,1,midg; midg,igrid,midg 8.4203063E-03 -1.1041185E-02 1,midg,midg; igrid,midg,midg 1.1720836E-02 5.4796296E-04 gauss-seidel spectral radius is 0.9981822 estimated iterations to convergence 186 setup time was (sec) 0.7100000 now iterating at: 14:14:45 rms-change max change #iterations 3.898651 149.2815 at 10iterations 1.625518 61.47174 at 20iterations 0.6784171 22.44418 at 30iterations 0.2822537 8.998390 at 40iterations 0.1181482 3.922215 at 50iterations 4.9258195E-02 1.671249 at 60iterations 2.0634346E-02 0.6721458 at 70iterations 8.7529169E-03 0.2694626 at 80iterations 3.7631979E-03 0.1299219 at 90iterations 1.6844029E-03 5.4845810E-02 at 100iterations 8.1852765E-04 3.1260490E-02 at 110iterations 4.6015266E-04 1.5869141E-02 at 120iterations finished qdiffx linear iterations at : 14:15:01 total time elapsed so far: 8.590000 # loops : 120 mean,max change (kT/e) : 4.6015266E-04 1.5869141E-02 energy calculations done at 8.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.720000 DelPhi exited at 14:15:02 8.722u 0.262s 0:17.39 51.6% 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 15 2011 at 14:15:02 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4638 !!! WARNING: HEM 807 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.342036 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): -24.71500 38.94200 ymin,ymax (A): -17.63100 45.00900 zmin,zma (A): 6.715000 75.11700 x,y,z range (A): 63.65700 62.64000 68.40201 scale (grids/A): 2.342036 object centre (A): 7.113501 13.68900 40.91600 number of atom coordinates read : 4638 total number of charged atoms : 4398 net assigned charge : 7.300036 assigned positive charge : 700.9634 centred at (gu) : 96.63473 85.80293 80.17529 assigned negative charge : -693.6675 centred at (gu) : 97.14283 86.30395 79.60569 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 207223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42782 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 95754 mr = 146630 m= 26714 mr = 74183 m= 3772 mr = 19604 m= 154 mr = 2175 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1379 time to turn everything in is 1.130000 number of dielectric boundary points 90988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 35110 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) : 1.561358 object centre at (A) : 7.113501 13.68900 40.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6020457 0.5051901 midg,1,midg; midg,igrid,midg 0.1254987 -0.2067883 1,midg,midg; igrid,midg,midg 0.1850596 1.5878404E-02 gauss-seidel spectral radius is 0.9991830 estimated iterations to convergence 276 setup time was (sec) 1.400000 now iterating at: 14:15:09 rms-change max change #iterations 10.48940 297.7777 at 10iterations 6.050621 149.3889 at 20iterations 3.470266 80.28743 at 30iterations 1.975852 42.45503 at 40iterations 1.121833 22.00172 at 50iterations 0.6351675 12.93535 at 60iterations 0.3585741 7.436966 at 70iterations 0.2017336 4.338974 at 80iterations 0.1136415 2.430199 at 90iterations 6.3817300E-02 1.297541 at 100iterations 3.5826918E-02 0.6160431 at 110iterations 2.0101152E-02 0.3781433 at 120iterations 1.1289611E-02 0.2490883 at 130iterations 6.3258731E-03 0.1236359 at 140iterations 3.5474757E-03 6.3594818E-02 at 150iterations 1.9893176E-03 3.9241791E-02 at 160iterations 1.1209013E-03 2.2203445E-02 at 170iterations 6.3390797E-04 1.5048981E-02 at 180iterations finished qdiffx linear iterations at : 14:15:34 total time elapsed so far: 14.15000 # loops : 180 mean,max change (kT/e) : 6.3390797E-04 1.5048981E-02 energy calculations done at 14.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 14:15:35 14.282u 0.264s 0:32.83 44.2% 0+0k 0+0io 0pf+0w