Sat Oct 8 16:01:11 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 8 2011 at 16:01:11 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 0.6475671 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 0.6475671 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.6781 centred at (gu) : 90.46924 88.74321 90.29971 assigned negative charge : -340.7788 centred at (gu) : 90.50629 88.86681 90.34850 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 47826 no. pairs analyzed = 47826 no. exposed pairs = 2797 no. arc points = 19701 no. surface atoms = 961 nbur = 1366 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3676 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1937 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2164366E-08 7.3512679E-10 midg,1,midg; midg,igrid,midg 2.8995053E-08 -6.6740999E-09 1,midg,midg; igrid,midg,midg 1.0424219E-08 2.3911311E-09 gauss-seidel spectral radius is 0.9876181 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 16:01:12 rms-change max change #iterations 0.1468966 28.31520 at 10iterations 1.4685684E-02 2.470181 at 20iterations 1.5236431E-03 0.2217579 at 30iterations 1.6588537E-04 2.5039673E-02 at 40iterations 2.2192817E-05 3.1564236E-03 at 50iterations finished qdiffx linear iterations at : 16:01:15 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.2192817E-05 3.1564236E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 16:01:16 4.514u 0.393s 0:05.21 94.0% 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 16:01:16 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 1.942701 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 1.942701 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.6781 centred at (gu) : 91.40744 86.22905 90.89840 assigned negative charge : -340.7788 centred at (gu) : 91.51878 86.60034 91.04543 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 25146 mr = 49438 m= 4337 mr = 18762 m= 282 mr = 2875 m= 2 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.5600000 number of dielectric boundary points 29156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17574 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) : 0.6475671 object centre at (A) : 22.02200 6.594000 8.886498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6559277E-02 -1.4697842E-02 midg,1,midg; midg,igrid,midg 2.8099602E-02 -5.4470967E-03 1,midg,midg; igrid,midg,midg 8.1923353E-03 -3.3293027E-02 gauss-seidel spectral radius is 0.9986567 estimated iterations to convergence 216 setup time was (sec) 0.9200000 now iterating at: 16:01:17 rms-change max change #iterations 4.150681 216.2380 at 10iterations 1.950907 74.30770 at 20iterations 0.9189669 29.18302 at 30iterations 0.4330739 15.47379 at 40iterations 0.2042824 6.711903 at 50iterations 9.6458040E-02 3.266018 at 60iterations 4.5371477E-02 1.434793 at 70iterations 2.1422792E-02 0.7327681 at 80iterations 1.0107546E-02 0.3137360 at 90iterations 4.7666300E-03 0.1489220 at 100iterations 2.2532172E-03 7.1773529E-02 at 110iterations 1.0643102E-03 3.3151627E-02 at 120iterations finished qdiffx linear iterations at : 16:01:27 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 1.0643102E-03 3.3151627E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 16:01:28 10.869u 0.440s 0:11.66 96.9% 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 16:01:28 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 2.914052 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): -1.971000 46.01500 ymin,ymax (A): -16.63500 29.82300 zmin,zma (A): -18.60100 36.37400 x,y,z range (A): 47.98600 46.45800 54.97500 scale (grids/A): 2.914052 object centre (A): 22.02200 6.594000 8.886498 number of atom coordinates read : 2327 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.6781 centred at (gu) : 92.11100 84.34354 91.34758 assigned negative charge : -340.7788 centred at (gu) : 92.27809 84.90047 91.56814 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 163774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 81177 mr = 120049 m= 29906 mr = 66802 m= 7926 mr = 24359 m= 1258 mr = 6260 m= 72 mr = 885 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 3432 time to turn everything in is 1.540000 number of dielectric boundary points 65722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 17838 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) : 1.942701 object centre at (A) : 22.02200 6.594000 8.886498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1720360 -0.1880086 midg,1,midg; midg,igrid,midg 0.2150699 -7.2423935E-02 1,midg,midg; igrid,midg,midg 8.1331596E-02 -0.4876603 gauss-seidel spectral radius is 0.9992566 estimated iterations to convergence 289 setup time was (sec) 1.870000 now iterating at: 16:01:30 rms-change max change #iterations 9.534742 515.1048 at 10iterations 5.556503 119.3761 at 20iterations 3.215012 70.99209 at 30iterations 1.865142 36.41304 at 40iterations 1.077615 21.19287 at 50iterations 0.6209045 11.96283 at 60iterations 0.3569160 6.450466 at 70iterations 0.2058341 4.050474 at 80iterations 0.1185018 2.201368 at 90iterations 6.8125248E-02 1.234670 at 100iterations 3.9246198E-02 0.7997971 at 110iterations 2.2496417E-02 0.4626920 at 120iterations 1.2921482E-02 0.2591963 at 130iterations 7.4301129E-03 0.1397190 at 140iterations 4.2764009E-03 7.7638626E-02 at 150iterations 2.4482608E-03 4.5564115E-02 at 160iterations 1.4077517E-03 2.6229858E-02 at 170iterations 8.0883404E-04 1.5338898E-02 at 180iterations finished qdiffx linear iterations at : 16:01:46 total time elapsed so far: 17.61000 # loops : 180 mean,max change (kT/e) : 8.0883404E-04 1.5338898E-02 energy calculations done at 17.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.78000 DelPhi exited at 16:01:46 17.780u 0.444s 0:18.50 98.4% 0+0k 0+0io 0pf+0w