Sat Oct 8 19:02:16 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 8 2011 at 19:02:16 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6262093 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 0.6262093 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.62567 89.24619 89.89534 assigned negative charge : -388.8955 centred at (gu) : 88.52055 89.28400 89.79076 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6717 nv = 96 ne = 84 npr = 54695 no. pairs analyzed = 54695 no. exposed pairs = 3036 no. arc points = 21637 no. surface atoms = 1010 nbur = 1594 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3787 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.3300000 number of dielectric boundary points 3221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2197 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0155794E-09 1.2406075E-08 midg,1,midg; midg,igrid,midg 8.8005425E-09 1.2758791E-09 1,midg,midg; igrid,midg,midg -5.4940408E-09 9.4562997E-09 gauss-seidel spectral radius is 0.9867885 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 19:02:17 rms-change max change #iterations 0.1347432 20.62470 at 10iterations 1.2836826E-02 1.847706 at 20iterations 1.2116407E-03 0.1979752 at 30iterations 1.1416237E-04 1.8733978E-02 at 40iterations 1.0771981E-05 1.5258789E-03 at 50iterations finished qdiffx linear iterations at : 19:02:21 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.0771981E-05 1.5258789E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 19:02:21 4.117u 0.319s 0:04.70 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 19:02:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.878628 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 1.878628 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.87674 87.73807 89.68533 assigned negative charge : -388.8955 centred at (gu) : 85.56147 87.85174 89.37197 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 25767 mr = 50941 m= 3823 mr = 19232 m= 190 mr = 2380 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 6208 time to turn everything in is 0.6500000 number of dielectric boundary points 29865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19343 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) : 0.6262093 object centre at (A) : -7.223499 -0.3245001 15.95100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9594762E-02 2.4218353E-02 midg,1,midg; midg,igrid,midg 1.4960878E-02 2.7200587E-03 1,midg,midg; igrid,midg,midg -4.1168835E-03 3.1992011E-02 gauss-seidel spectral radius is 0.9985956 estimated iterations to convergence 212 setup time was (sec) 0.9200000 now iterating at: 19:02:22 rms-change max change #iterations 4.145632 230.6882 at 10iterations 1.919770 71.56448 at 20iterations 0.8895262 27.53867 at 30iterations 0.4104148 14.26891 at 40iterations 0.1909353 6.024630 at 50iterations 8.8515989E-02 2.801094 at 60iterations 4.1003451E-02 1.473755 at 70iterations 1.8989315E-02 0.5916080 at 80iterations 8.8022556E-03 0.2864590 at 90iterations 4.0745283E-03 0.1390991 at 100iterations 1.8926414E-03 6.0806274E-02 at 110iterations 8.7483728E-04 2.8345108E-02 at 120iterations finished qdiffx linear iterations at : 19:02:31 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 8.7483728E-04 2.8345108E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 19:02:31 9.586u 0.347s 0:10.24 96.8% 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 19:02:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2604 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.817942 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): -32.04400 17.59700 ymin,ymax (A): -23.44400 22.79500 zmin,zma (A): -12.47400 44.37600 x,y,z range (A): 49.64100 46.23900 56.85000 scale (grids/A): 2.817942 object centre (A): -7.223499 -0.3245001 15.95100 number of atom coordinates read : 2604 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.81501 86.60690 89.52789 assigned negative charge : -388.8955 centred at (gu) : 83.34231 86.77747 89.05804 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 168040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 84810 mr = 123301 m= 29667 mr = 70057 m= 6882 mr = 23874 m= 906 mr = 5150 m= 35 mr = 610 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 21507 time to turn everything in is 1.630000 number of dielectric boundary points 67338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19728 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) : 1.878628 object centre at (A) : -7.223499 -0.3245001 15.95100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1338644 0.2925619 midg,1,midg; midg,igrid,midg 0.1743506 3.0799596E-02 1,midg,midg; igrid,midg,midg -3.7047405E-02 0.3957587 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.940000 now iterating at: 19:02:34 rms-change max change #iterations 9.624525 356.6461 at 10iterations 5.542172 113.6772 at 20iterations 3.167615 64.40574 at 30iterations 1.807563 37.35893 at 40iterations 1.034623 18.47925 at 50iterations 0.5894518 10.33580 at 60iterations 0.3362846 6.232006 at 70iterations 0.1922661 3.607752 at 80iterations 0.1094192 2.017365 at 90iterations 6.2410209E-02 1.194736 at 100iterations 3.5619479E-02 0.6991024 at 110iterations 2.0288475E-02 0.3815498 at 120iterations 1.1565600E-02 0.2565155 at 130iterations 6.6061113E-03 0.1197815 at 140iterations 3.7597895E-03 6.8503380E-02 at 150iterations 2.1462666E-03 3.7767410E-02 at 160iterations 1.2226586E-03 2.2629499E-02 at 170iterations 6.9745805E-04 1.2526035E-02 at 180iterations finished qdiffx linear iterations at : 19:02:48 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 6.9745805E-04 1.2526035E-02 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.07000 DelPhi exited at 19:02:48 16.073u 0.341s 0:16.69 98.3% 0+0k 0+0io 0pf+0w