Sat Oct 15 14:45:35 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 Sat Oct 15 2011 at 14:45:35 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 0.5479789 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 0.5479789 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.485979 assigned positive charge : 453.4970 centred at (gu) : 89.38179 90.02620 89.73109 assigned negative charge : -454.9841 centred at (gu) : 89.32932 89.90949 89.62515 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5816 nv = 96 ne = 84 npr = 60503 no. pairs analyzed = 60503 no. exposed pairs = 3895 no. arc points = 27582 no. surface atoms = 1316 nbur = 1697 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 = 1.596000 m= 223 mr = 2889 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2881 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4242159E-10 6.2791633E-10 midg,1,midg; midg,igrid,midg -9.5592367E-10 7.5366807E-10 1,midg,midg; igrid,midg,midg -5.6159893E-10 2.4595015E-10 gauss-seidel spectral radius is 0.9828365 estimated iterations to convergence 63 setup time was (sec) 0.4300000 now iterating at: 14:45:36 rms-change max change #iterations 7.5829856E-02 12.59305 at 10iterations 5.0780731E-03 0.7822647 at 20iterations 3.3177561E-04 6.7781448E-02 at 30iterations 2.2652610E-05 3.6525726E-03 at 40iterations 1.5571545E-06 2.7084351E-04 at 50iterations finished qdiffx linear iterations at : 14:45:40 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.5571545E-06 2.7084351E-04 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 14:45:40 3.700u 0.228s 0:04.69 83.5% 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 14:45:40 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 1.643937 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 1.643937 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.485979 assigned positive charge : 453.4970 centred at (gu) : 88.14436 90.07794 89.19225 assigned negative charge : -454.9841 centred at (gu) : 87.98765 89.72809 88.87529 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19113 mr = 43215 m= 1836 mr = 12775 m= 51 mr = 800 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 658 time to turn everything in is 0.3200000 number of dielectric boundary points 29331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 22042 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) : 0.5479789 object centre at (A) : 15.17800 -5.340000 -19.26500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7259514E-02 5.2477871E-03 midg,1,midg; midg,igrid,midg -3.1133872E-03 5.0107157E-03 1,midg,midg; igrid,midg,midg -2.0616626E-02 7.0997449E-03 gauss-seidel spectral radius is 0.9982172 estimated iterations to convergence 188 setup time was (sec) 0.5500000 now iterating at: 14:45:41 rms-change max change #iterations 3.414023 163.7504 at 10iterations 1.431298 54.32429 at 20iterations 0.6000900 20.97224 at 30iterations 0.2518165 8.806540 at 40iterations 0.1053777 3.928436 at 50iterations 4.4361822E-02 1.596745 at 60iterations 1.8651860E-02 0.6575160 at 70iterations 7.8177005E-03 0.2619944 at 80iterations 3.2808532E-03 0.1280432 at 90iterations 1.3790765E-03 5.1910400E-02 at 100iterations 5.7849608E-04 2.2506714E-02 at 110iterations 2.4302589E-04 8.7509155E-03 at 120iterations finished qdiffx linear iterations at : 14:45:52 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 2.4302589E-04 8.7509155E-03 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 14:45:53 8.326u 0.274s 0:12.56 68.3% 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 Sat Oct 15 2011 at 14:45:53 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 2.465905 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 2.465905 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.485979 assigned positive charge : 453.4970 centred at (gu) : 87.21638 90.11671 88.78822 assigned negative charge : -454.9841 centred at (gu) : 86.98147 89.59197 88.31277 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 151394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66778 mr = 106178 m= 18249 mr = 52000 m= 2766 mr = 13262 m= 140 mr = 1630 m= 0 mr = 35 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2144 time to turn everything in is 0.8200000 number of dielectric boundary points 66222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 22938 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) : 1.643937 object centre at (A) : 15.17800 -5.340000 -19.26500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2606491 9.8382547E-02 midg,1,midg; midg,igrid,midg -4.2455569E-02 5.5230472E-02 1,midg,midg; igrid,midg,midg -0.7211568 0.3442839 gauss-seidel spectral radius is 0.9991528 estimated iterations to convergence 271 setup time was (sec) 1.130000 now iterating at: 14:45:54 rms-change max change #iterations 8.866532 294.2308 at 10iterations 4.979441 149.3647 at 20iterations 2.781741 67.74780 at 30iterations 1.549002 37.40216 at 40iterations 0.8599977 18.36166 at 50iterations 0.4758173 9.706696 at 60iterations 0.2635098 6.110809 at 70iterations 0.1454388 3.299535 at 80iterations 8.0300681E-02 1.883547 at 90iterations 4.4345811E-02 0.9465122 at 100iterations 2.4516031E-02 0.5616760 at 110iterations 1.3520073E-02 0.2977600 at 120iterations 7.4401973E-03 0.1520367 at 130iterations 4.1060578E-03 8.2773685E-02 at 140iterations 2.2697879E-03 4.7916412E-02 at 150iterations 1.2497429E-03 2.5684834E-02 at 160iterations 6.8924983E-04 1.4366150E-02 at 170iterations 3.8046599E-04 7.9784393E-03 at 180iterations finished qdiffx linear iterations at : 14:46:10 total time elapsed so far: 14.19000 # loops : 180 mean,max change (kT/e) : 3.8046599E-04 7.9784393E-03 energy calculations done at 14.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.33000 DelPhi exited at 14:46:11 14.328u 0.314s 0:17.77 82.3% 0+0k 0+0io 0pf+0w