Mon Oct 10 14:14:37 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 14:14:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5814524 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 0.5814524 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 408.1266 centred at (gu) : 92.20387 89.94984 89.30937 assigned negative charge : -412.7274 centred at (gu) : 92.18086 90.02171 89.37518 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 51226 no. pairs analyzed = 51226 no. exposed pairs = 3703 no. arc points = 25783 no. surface atoms = 1246 nbur = 1393 mkacc time = 9.0000004E-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 = 1.512000 m= 286 mr = 2918 m= 0 mr = 26 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8567072E-10 -2.1195032E-09 midg,1,midg; midg,igrid,midg 4.5157553E-10 -2.5886004E-09 1,midg,midg; igrid,midg,midg -9.4937769E-10 -9.4740948E-10 gauss-seidel spectral radius is 0.9847118 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 14:14:37 rms-change max change #iterations 9.7797170E-02 16.98310 at 10iterations 7.5876703E-03 1.282745 at 20iterations 6.1094388E-04 0.1010666 at 30iterations 5.9409456E-05 9.7274780E-03 at 40iterations 1.1804472E-05 2.1065474E-03 at 50iterations finished qdiffx linear iterations at : 14:14:40 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1804472E-05 2.1065474E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:14:41 3.363u 0.167s 0:04.04 87.1% 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 14:14:41 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.744357 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 1.744357 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 408.1266 centred at (gu) : 96.61100 89.84885 87.92738 assigned negative charge : -412.7274 centred at (gu) : 96.54231 90.06502 88.12506 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25783 grid for indexing accessible points = 1.400000 m= 21561 mr = 42416 m= 2869 mr = 14522 m= 139 mr = 1478 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 30966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19353 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) : 0.5814524 object centre at (A) : 21.79600 9.246500 104.9720 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1576788E-02 -2.3947837E-02 midg,1,midg; midg,igrid,midg -3.8285195E-03 -1.4123802E-02 1,midg,midg; igrid,midg,midg 2.0991873E-02 1.8070551E-02 gauss-seidel spectral radius is 0.9983964 estimated iterations to convergence 198 setup time was (sec) 0.5900000 now iterating at: 14:14:42 rms-change max change #iterations 3.724325 197.4112 at 10iterations 1.620779 66.31264 at 20iterations 0.7136010 27.81063 at 30iterations 0.3123277 12.24757 at 40iterations 0.1374144 5.027402 at 50iterations 6.0410399E-02 2.175997 at 60iterations 2.6509590E-02 0.9459012 at 70iterations 1.1613493E-02 0.4575157 at 80iterations 5.1099476E-03 0.1983719 at 90iterations 2.2491922E-03 8.3227158E-02 at 100iterations 9.8891824E-04 3.4332275E-02 at 110iterations 4.3597605E-04 1.5199482E-02 at 120iterations finished qdiffx linear iterations at : 14:14:49 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 4.3597605E-04 1.5199482E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 14:14:50 7.989u 0.258s 0:08.74 94.1% 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 14:14:50 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 !!! WARNING: ADP 670 has a net charge of -2.0000 !!! WARNING: MG6 672 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.616536 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): -8.816999 52.40900 ymin,ymax (A): -15.91700 34.41000 zmin,zma (A): 79.22800 130.7160 x,y,z range (A): 61.22600 50.32700 51.48800 scale (grids/A): 2.616536 object centre (A): 21.79600 9.246500 104.9720 number of atom coordinates read : 2639 total number of charged atoms : 2497 net assigned charge : -4.599992 assigned positive charge : 408.1266 centred at (gu) : 99.91625 89.77305 86.89080 assigned negative charge : -412.7274 centred at (gu) : 99.81345 90.09757 87.18768 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25783 grid for indexing accessible points = 1.400000 m= 71212 mr = 104290 m= 23131 mr = 55236 m= 4729 mr = 17052 m= 526 mr = 3116 m= 26 mr = 322 m= 0 mr = 3 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 69846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 19967 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) : 1.744357 object centre at (A) : 21.79600 9.246500 104.9720 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1490931 -0.3044248 midg,1,midg; midg,igrid,midg -7.7490665E-02 -0.1218782 1,midg,midg; igrid,midg,midg 0.3416869 0.1663734 gauss-seidel spectral radius is 0.9992023 estimated iterations to convergence 280 setup time was (sec) 1.060000 now iterating at: 14:14:51 rms-change max change #iterations 9.404272 336.1677 at 10iterations 5.499473 152.3391 at 20iterations 3.172438 79.13789 at 30iterations 1.817355 40.02868 at 40iterations 1.039429 22.04773 at 50iterations 0.5906339 12.92992 at 60iterations 0.3349425 7.563929 at 70iterations 0.1897995 3.791737 at 80iterations 0.1073104 2.225010 at 90iterations 6.0511865E-02 1.210639 at 100iterations 3.4205008E-02 0.6903291 at 110iterations 1.9243797E-02 0.4225693 at 120iterations 1.0852524E-02 0.2160854 at 130iterations 6.1216494E-03 0.1379929 at 140iterations 3.4447480E-03 6.7792892E-02 at 150iterations 1.9422128E-03 4.6325684E-02 at 160iterations 1.0968460E-03 2.1960735E-02 at 170iterations 6.2016817E-04 1.3549805E-02 at 180iterations finished qdiffx linear iterations at : 14:15:02 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 6.2016817E-04 1.3549805E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 14:15:03 12.424u 0.242s 0:13.15 96.2% 0+0k 0+0io 0pf+0w