Sat Oct 15 12:39:10 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 12:39:10 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: NDP 1049 has a net charge of -3.0000 !!! WARNING: NDP 1050 has a net charge of -3.0000 !!! WARNING: NDP 1051 has a net charge of -3.0000 !!! WARNING: NDP 1052 has a net charge of -3.0000 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: 0.4534801 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): -74.32700 -17.11400 ymin,ymax (A): -96.33500 -17.83100 zmin,zma (A): -43.74600 22.41700 x,y,z range (A): 57.21301 78.50400 66.16299 scale (grids/A): 0.4534801 object centre (A): -45.72050 -57.08300 -10.66450 number of atom coordinates read : 4218 total number of charged atoms : 4065 net assigned charge : -12.99999 assigned positive charge : 638.3408 centred at (gu) : 89.47966 89.71815 90.31740 assigned negative charge : -651.3436 centred at (gu) : 89.48636 89.71306 90.30333 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5668 nv = 96 ne = 84 npr = 78158 no. pairs analyzed = 78158 no. exposed pairs = 6793 no. arc points = 49123 no. surface atoms = 2238 nbur = 1980 mkacc time = 0.2100000 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 = 1.848000 m= 189 mr = 2124 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4341 ## 872 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1582947E-11 -9.2259577E-12 midg,1,midg; midg,igrid,midg -1.2286158E-11 -9.0295306E-12 1,midg,midg; igrid,midg,midg -1.1076662E-11 -9.9671538E-12 gauss-seidel spectral radius is 0.9751802 estimated iterations to convergence 53 setup time was (sec) 0.7700000 now iterating at: 12:39:12 rms-change max change #iterations 2.9981622E-02 6.669308 at 10iterations 1.1798014E-03 0.1969318 at 20iterations 7.3818919E-05 1.2758255E-02 at 30iterations 1.4934801E-05 2.3727417E-03 at 40iterations 3.8483049E-06 6.1774254E-04 at 50iterations finished qdiffx linear iterations at : 12:39:16 total time elapsed so far: 5.340000 # loops : 50 mean,max change (kT/e) : 3.8483049E-06 6.1774254E-04 energy calculations done at 5.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.510000 DelPhi exited at 12:39:17 5.519u 0.453s 0:06.45 92.4% 0+0k 0+0io 6pf+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 12:39:17 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: NDP 1049 has a net charge of -3.0000 !!! WARNING: NDP 1050 has a net charge of -3.0000 !!! WARNING: NDP 1051 has a net charge of -3.0000 !!! WARNING: NDP 1052 has a net charge of -3.0000 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: 1.360440 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): -74.32700 -17.11400 ymin,ymax (A): -96.33500 -17.83100 zmin,zma (A): -43.74600 22.41700 x,y,z range (A): 57.21301 78.50400 66.16299 scale (grids/A): 1.360440 object centre (A): -45.72050 -57.08300 -10.66450 number of atom coordinates read : 4218 total number of charged atoms : 4065 net assigned charge : -12.99999 assigned positive charge : 638.3408 centred at (gu) : 88.43780 89.15353 90.95107 assigned negative charge : -651.3436 centred at (gu) : 88.45869 89.13889 90.90985 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 13839 mr = 36733 m= 871 mr = 6926 m= 12 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 699 ## 23 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 29236 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) : 0.4534801 object centre at (A) : -45.72050 -57.08300 -10.66450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1178954E-03 -1.3620526E-03 midg,1,midg; midg,igrid,midg -4.9782614E-03 -9.9544823E-03 1,midg,midg; igrid,midg,midg -2.6425256E-03 -1.7986725E-03 gauss-seidel spectral radius is 0.9975223 estimated iterations to convergence 160 setup time was (sec) 0.9300000 now iterating at: 12:39:18 rms-change max change #iterations 2.711910 187.0363 at 10iterations 0.9625385 56.47191 at 20iterations 0.3431700 18.44743 at 30iterations 0.1220193 6.541183 at 40iterations 4.3543868E-02 1.917496 at 50iterations 1.5540850E-02 0.6028299 at 60iterations 5.5573997E-03 0.2320529 at 70iterations 1.9982764E-03 9.2796803E-02 at 80iterations 7.1943749E-04 2.9973269E-02 at 90iterations 2.5966993E-04 1.0194778E-02 at 100iterations 9.4642237E-05 3.8906336E-03 at 110iterations 3.5515128E-05 1.5832186E-03 at 120iterations finished qdiffx linear iterations at : 12:39:31 total time elapsed so far: 12.36000 # loops : 120 mean,max change (kT/e) : 3.5515128E-05 1.5832186E-03 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 12:39:32 12.540u 0.521s 0:15.11 86.4% 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 12:39:32 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4218 !!! WARNING: NDP 1049 has a net charge of -3.0000 !!! WARNING: NDP 1050 has a net charge of -3.0000 !!! WARNING: NDP 1051 has a net charge of -3.0000 !!! WARNING: NDP 1052 has a net charge of -3.0000 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: 2.040660 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): -74.32700 -17.11400 ymin,ymax (A): -96.33500 -17.83100 zmin,zma (A): -43.74600 22.41700 x,y,z range (A): 57.21301 78.50400 66.16299 scale (grids/A): 2.040660 object centre (A): -45.72050 -57.08300 -10.66450 number of atom coordinates read : 4218 total number of charged atoms : 4065 net assigned charge : -12.99999 assigned positive charge : 638.3408 centred at (gu) : 87.65639 88.73007 91.42614 assigned negative charge : -651.3436 centred at (gu) : 87.68794 88.70817 91.36461 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 150179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 52043 mr = 93318 m= 9615 mr = 34396 m= 934 mr = 5419 m= 30 mr = 409 m= 0 mr = 0 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 79259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 32244 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) : 1.360440 object centre at (A) : -45.72050 -57.08300 -10.66450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1082613 7.8313546E-03 midg,1,midg; midg,igrid,midg 2.5005413E-02 -0.2333203 1,midg,midg; igrid,midg,midg -4.3484095E-02 -2.3700185E-02 gauss-seidel spectral radius is 0.9989728 estimated iterations to convergence 247 setup time was (sec) 1.750000 now iterating at: 12:39:34 rms-change max change #iterations 8.287989 307.4253 at 10iterations 4.535445 148.2543 at 20iterations 2.445632 82.63987 at 30iterations 1.308365 39.32355 at 40iterations 0.6970431 17.39030 at 50iterations 0.3693048 9.453445 at 60iterations 0.1954106 5.022833 at 70iterations 0.1026565 3.034380 at 80iterations 5.3900231E-02 1.338394 at 90iterations 2.8320232E-02 0.7199249 at 100iterations 1.4820442E-02 0.3830051 at 110iterations 7.7285510E-03 0.2087989 at 120iterations 4.0344442E-03 0.1122857 at 130iterations 2.1099215E-03 5.7786942E-02 at 140iterations 1.0988645E-03 2.7954102E-02 at 150iterations 5.7366217E-04 1.5967250E-02 at 160iterations 2.9909253E-04 7.6926947E-03 at 170iterations 1.5608019E-04 4.2114258E-03 at 180iterations finished qdiffx linear iterations at : 12:39:57 total time elapsed so far: 21.17000 # loops : 180 mean,max change (kT/e) : 1.5608019E-04 4.2114258E-03 energy calculations done at 21.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.34000 DelPhi exited at 12:39:57 21.346u 0.529s 0:25.40 86.0% 0+0k 0+0io 0pf+0w