Sun Oct 9 06:52:14 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 Sun Oct 9 2011 at 06:52:14 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6674165 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): -40.95700 1.867000 ymin,ymax (A): -12.74000 33.41200 zmin,zma (A): -55.89800 -2.558000 x,y,z range (A): 42.82400 46.15200 53.34000 scale (grids/A): 0.6674165 object centre (A): -19.54500 10.33600 -29.22800 number of atom coordinates read : 2003 total number of charged atoms : 1864 net assigned charge : -1.499988 assigned positive charge : 299.0360 centred at (gu) : 89.89203 90.97224 91.48557 assigned negative charge : -300.5361 centred at (gu) : 89.72395 91.15383 91.53246 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6028 nv = 96 ne = 84 npr = 42354 no. pairs analyzed = 42354 no. exposed pairs = 2449 no. arc points = 17491 no. surface atoms = 832 nbur = 1171 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3300 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.1700000 number of dielectric boundary points 3001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2956458E-09 -1.7301439E-08 midg,1,midg; midg,igrid,midg 2.3461521E-08 -4.6769507E-08 1,midg,midg; igrid,midg,midg -3.6348194E-08 2.5798281E-08 gauss-seidel spectral radius is 0.9883080 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 06:52:15 rms-change max change #iterations 0.1542710 24.44258 at 10iterations 1.6866695E-02 2.639076 at 20iterations 1.8116444E-03 0.2740612 at 30iterations 1.9585545E-04 3.3847809E-02 at 40iterations 2.1389998E-05 2.9582977E-03 at 50iterations finished qdiffx linear iterations at : 06:52:18 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 2.1389998E-05 2.9582977E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 06:52:19 3.573u 0.221s 0:04.06 93.3% 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 Sun Oct 9 2011 at 06:52:19 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.002249 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): -40.95700 1.867000 ymin,ymax (A): -12.74000 33.41200 zmin,zma (A): -55.89800 -2.558000 x,y,z range (A): 42.82400 46.15200 53.34000 scale (grids/A): 2.002249 object centre (A): -19.54500 10.33600 -29.22800 number of atom coordinates read : 2003 total number of charged atoms : 1864 net assigned charge : -1.499988 assigned positive charge : 299.0360 centred at (gu) : 89.67624 92.91671 94.45683 assigned negative charge : -300.5361 centred at (gu) : 89.17199 93.46149 94.59748 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 22882 mr = 44288 m= 4000 mr = 16960 m= 253 mr = 2640 m= 6 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3566 time to turn everything in is 0.3300000 number of dielectric boundary points 27348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14761 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) : 0.6674165 object centre at (A) : -19.54500 10.33600 -29.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7659127E-02 -4.7696743E-02 midg,1,midg; midg,igrid,midg 1.7241430E-02 -3.3178300E-02 1,midg,midg; igrid,midg,midg -2.4831636E-02 1.9421598E-02 gauss-seidel spectral radius is 0.9986979 estimated iterations to convergence 220 setup time was (sec) 0.5600000 now iterating at: 06:52:19 rms-change max change #iterations 4.137409 201.3475 at 10iterations 1.965871 82.01306 at 20iterations 0.9342996 31.75610 at 30iterations 0.4437457 16.23621 at 40iterations 0.2115160 7.027090 at 50iterations 0.1009286 3.332192 at 60iterations 4.8231527E-02 1.524956 at 70iterations 2.2892442E-02 0.7374039 at 80iterations 1.0908248E-02 0.3977098 at 90iterations 5.1954184E-03 0.1811123 at 100iterations 2.4713352E-03 8.2410812E-02 at 110iterations 1.1824691E-03 4.1664124E-02 at 120iterations finished qdiffx linear iterations at : 06:52:27 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.1824691E-03 4.1664124E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 06:52:27 8.016u 0.228s 0:08.52 96.5% 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 Sun Oct 9 2011 at 06:52:27 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.003374 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): -40.95700 1.867000 ymin,ymax (A): -12.74000 33.41200 zmin,zma (A): -55.89800 -2.558000 x,y,z range (A): 42.82400 46.15200 53.34000 scale (grids/A): 3.003374 object centre (A): -19.54500 10.33600 -29.22800 number of atom coordinates read : 2003 total number of charged atoms : 1864 net assigned charge : -1.499988 assigned positive charge : 299.0360 centred at (gu) : 89.51421 94.37512 96.68526 assigned negative charge : -300.5361 centred at (gu) : 88.75790 95.19228 96.89632 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 74184 mr = 106956 m= 26813 mr = 60943 m= 7289 mr = 21679 m= 1311 mr = 5676 m= 95 mr = 933 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 11975 time to turn everything in is 0.8400000 number of dielectric boundary points 61779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14912 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) : 2.002249 object centre at (A) : -19.54500 10.33600 -29.22800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8662436 -0.5148489 midg,1,midg; midg,igrid,midg 0.1958796 -0.2427969 1,midg,midg; igrid,midg,midg -0.2093091 0.1726154 gauss-seidel spectral radius is 0.9992595 estimated iterations to convergence 290 setup time was (sec) 1.080000 now iterating at: 06:52:28 rms-change max change #iterations 9.389758 431.7568 at 10iterations 5.384505 124.8214 at 20iterations 3.094941 58.12834 at 30iterations 1.779196 34.29741 at 40iterations 1.016334 18.42940 at 50iterations 0.5852805 11.25962 at 60iterations 0.3345124 6.603138 at 70iterations 0.1916315 3.738381 at 80iterations 0.1101345 2.146933 at 90iterations 6.3084766E-02 1.246385 at 100iterations 3.6222689E-02 0.7191138 at 110iterations 2.0723607E-02 0.3892756 at 120iterations 1.1889909E-02 0.2281570 at 130iterations 6.8195579E-03 0.1277336 at 140iterations 3.9066030E-03 7.9801083E-02 at 150iterations 2.2436457E-03 4.2560577E-02 at 160iterations 1.2877317E-03 2.4440765E-02 at 170iterations 7.4077264E-04 1.4175415E-02 at 180iterations finished qdiffx linear iterations at : 06:52:40 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 7.4077264E-04 1.4175415E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 06:52:40 12.778u 0.219s 0:13.31 97.5% 0+0k 0+0io 0pf+0w